2V2L

Mutant (E53,56,57,60Q) 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 0.13M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE 0.1M PH 5.5, SODIUM AZIDE 0.003M. DROP: 2 UL PROTEIN AND 2 UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
3.261.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.455α = 90
b = 182.455β = 90
c = 182.455γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHTWO MIRRORS ARE USED FOR VERTICAL FOCUSSING.2003-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
11.9201000.0637.110.521041
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)
11.91.9499.90.495.37

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 2V2I1.9105.4119645106498.20.190.1880.216RANDOM19.95
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_deg37.377
r_dihedral_angle_4_deg19.804
r_dihedral_angle_3_deg13.44
r_dihedral_angle_1_deg5.435
r_scangle_it4.763
r_scbond_it3.459
r_mcangle_it1.758
r_mcbond_it1.664
r_angle_refined_deg1.556
r_angle_other_deg0.991
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.377
r_dihedral_angle_4_deg19.804
r_dihedral_angle_3_deg13.44
r_dihedral_angle_1_deg5.435
r_scangle_it4.763
r_scbond_it3.459
r_mcangle_it1.758
r_mcbond_it1.664
r_angle_refined_deg1.556
r_angle_other_deg0.991
r_symmetry_vdw_other0.267
r_nbd_refined0.239
r_symmetry_vdw_refined0.233
r_nbd_other0.193
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.146
r_chiral_restr0.102
r_nbtor_other0.088
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 Atoms1372
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling