7EMV

Crystal Structure of the HasAp V37G Mutant Capturing Iron-5,10,15-Triphenylporphyrin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293100mM Imidazole/HCl (pH 8.0), 30% PEG 8000, 0.2M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.1643.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.347α = 90
b = 84.347β = 90
c = 45.735γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2018-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.4545.7499.60.0870.0890.01712525.929690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4792.91.4611.5190.4090.55213.5

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 REPLACEMENTTHROUGHOUT5XIC1.452028084154099.380.13190.12940.176RANDOM18.55
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]
0.290.29-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.914
r_dihedral_angle_3_deg10.478
r_dihedral_angle_1_deg6.691
r_rigid_bond_restr4.238
r_dihedral_angle_4_deg2.731
r_angle_refined_deg1.888
r_angle_other_deg1.658
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.914
r_dihedral_angle_3_deg10.478
r_dihedral_angle_1_deg6.691
r_rigid_bond_restr4.238
r_dihedral_angle_4_deg2.731
r_angle_refined_deg1.888
r_angle_other_deg1.658
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1326
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms60

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing