7EMT

Crystal Structure of the HasAp V37G Mutant Capturing Iron Tetraphenylporphyrin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ELL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.629350mM Citric acid/NaOH (pH 3.6), 10% PEG 1000
Crystal Properties
Matthews coefficientSolvent content
2.7955.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.978α = 90
b = 60.757β = 90
c = 64.229γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2019-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.000SPring-8BL26B1

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
11.844.141000.040.0410.011129.813.219112
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)
11.81.8499.62.4172.5240.7180.60612

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 REPLACEMENTTHROUGHOUT3ELL1.82018028101999.870.2120.21150.2212RANDOM46.19
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]
-2.35.33-3.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg35.497
r_dihedral_angle_2_deg33.164
r_dihedral_angle_3_deg13.471
r_dihedral_angle_1_deg7.462
r_angle_refined_deg1.38
r_angle_other_deg1.287
r_chiral_restr0.045
r_gen_planes_refined0.015
r_gen_planes_other0.008
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg35.497
r_dihedral_angle_2_deg33.164
r_dihedral_angle_3_deg13.471
r_dihedral_angle_1_deg7.462
r_angle_refined_deg1.38
r_angle_other_deg1.287
r_chiral_restr0.045
r_gen_planes_refined0.015
r_gen_planes_other0.008
r_bond_refined_d0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1259
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms49

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing