2V2N

Mutant R59M recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V2IPDB ENTRY 2V2I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 1.1M, SODIUM ACETATE 0.1M PH 5.6, SODIUM AZIDE 0.003M DROP: 1UL PROTEIN AND 1UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
3.160.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.902α = 90
b = 181.902β = 90
c = 181.902γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRROR 2 BENT, VERTICALLY FOCUSSING2006-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.551296.40.0616.84.736531
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.688.10.443.54.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2V2I1.55104.83347401823970.190.1890.222RANDOM14.81
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.628
r_dihedral_angle_4_deg22.019
r_dihedral_angle_3_deg13.564
r_scangle_it4.819
r_dihedral_angle_1_deg4.668
r_scbond_it3.364
r_mcangle_it1.761
r_mcbond_it1.667
r_angle_refined_deg1.601
r_angle_other_deg0.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.628
r_dihedral_angle_4_deg22.019
r_dihedral_angle_3_deg13.564
r_scangle_it4.819
r_dihedral_angle_1_deg4.668
r_scbond_it3.364
r_mcangle_it1.761
r_mcbond_it1.667
r_angle_refined_deg1.601
r_angle_other_deg0.965
r_symmetry_vdw_refined0.39
r_symmetry_vdw_other0.262
r_nbd_refined0.254
r_xyhbond_nbd_refined0.214
r_nbd_other0.196
r_nbtor_refined0.187
r_symmetry_hbond_refined0.132
r_chiral_restr0.1
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1366
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling