2V2R

Mutant (E53,56,57,60Q and R59M) recombinant horse spleen apoferritin cocrystallized with haemin in basic conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V2PPDB ENTRY 2V2P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2RESERVOIR: CADMIUM SULFATE 0.16M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 8.2
Crystal Properties
Matthews coefficientSolvent content
3.261.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.589α = 90
b = 183.589β = 90
c = 183.589γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRROR 1, FLAT PRE-MIRROR, MIRROR 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
11.92098.90.0914.96.921258
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)
11.9299.90.534.27.1

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 2V2P1.910620161108698.90.190.1880.23RANDOM19.28
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_deg37.631
r_dihedral_angle_4_deg19.366
r_dihedral_angle_3_deg14.083
r_dihedral_angle_1_deg5.362
r_scangle_it4.771
r_scbond_it3.526
r_mcangle_it1.814
r_mcbond_it1.741
r_angle_refined_deg1.633
r_angle_other_deg1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.631
r_dihedral_angle_4_deg19.366
r_dihedral_angle_3_deg14.083
r_dihedral_angle_1_deg5.362
r_scangle_it4.771
r_scbond_it3.526
r_mcangle_it1.814
r_mcbond_it1.741
r_angle_refined_deg1.633
r_angle_other_deg1.08
r_symmetry_vdw_other0.28
r_nbd_refined0.237
r_symmetry_vdw_refined0.207
r_nbd_other0.193
r_xyhbond_nbd_refined0.191
r_nbtor_refined0.183
r_symmetry_hbond_refined0.157
r_chiral_restr0.13
r_nbtor_other0.091
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms1369
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling