Experiment: 2BDX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JK7	PDB ID 1JK7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	273	2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%) and beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.978	α = 90
b = 99.978	β = 90
c = 62.949	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4	mirrors	2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	100	99.9	0.067	0.067	8.5	7.7		14724		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	100	100	0.267	0.267	2.5	7.6	2101

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 1JK7	2.3	35.36	3	14689	739	99.94	0.214	0.214	0.212	0.25	RANDOM	32.699

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.05			-0.05		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.223
r_dihedral_angle_4_deg	18.294
r_dihedral_angle_3_deg	15.76
r_dihedral_angle_1_deg	7.182
r_scangle_it	3.016
r_scbond_it	2.02
r_mcangle_it	1.63
r_angle_refined_deg	1.574
r_mcbond_it	0.948
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.223
r_dihedral_angle_4_deg	18.294
r_dihedral_angle_3_deg	15.76
r_dihedral_angle_1_deg	7.182
r_scangle_it	3.016
r_scbond_it	2.02
r_mcangle_it	1.63
r_angle_refined_deg	1.574
r_mcbond_it	0.948
r_nbtor_refined	0.302
r_xyhbond_nbd_refined	0.162
r_nbd_refined	0.147
r_symmetry_hbond_refined	0.13
r_symmetry_vdw_refined	0.122
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2403
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.