2V2P

Mutant (E53,56,57,60Q and 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 2V2LPDB ENTRY 2V2L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5RESERVOIR: CADMIUM SULFATE 0.08M, AMMONIUM SULFATE 0.5M, SODIUM ACETATE 0.1M PH 5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
3.160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.255α = 90
b = 181.255β = 90
c = 181.255γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR 2 BENT, VERTICALLY FOCUSSING2007-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.152398.40.06146.888729
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)
11.151.287.80.4633.8

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 2V2L1.15104.8384284444098.70.2010.1990.224RANDOM11.58
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_deg37.935
r_dihedral_angle_4_deg17.96
r_dihedral_angle_3_deg11.437
r_scangle_it5.836
r_dihedral_angle_1_deg4.695
r_scbond_it4.421
r_mcangle_it2.593
r_mcbond_it2.366
r_angle_refined_deg1.666
r_angle_other_deg0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.935
r_dihedral_angle_4_deg17.96
r_dihedral_angle_3_deg11.437
r_scangle_it5.836
r_dihedral_angle_1_deg4.695
r_scbond_it4.421
r_mcangle_it2.593
r_mcbond_it2.366
r_angle_refined_deg1.666
r_angle_other_deg0.981
r_nbd_refined0.266
r_symmetry_vdw_refined0.262
r_symmetry_vdw_other0.241
r_xyhbond_nbd_refined0.22
r_nbd_other0.204
r_nbtor_refined0.19
r_symmetry_hbond_refined0.18
r_chiral_restr0.105
r_nbtor_other0.093
r_bond_refined_d0.018
r_gen_planes_refined0.008
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 Atoms1360
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling