7EMU

Crystal Structure of the HasAp V37G Mutant Capturing Manganese 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
2.6854.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.037α = 90
b = 62.233β = 90
c = 63.383γ = 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
11.3539.899.90.0450.0470.012127.814.445004
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)
11.351.371002.1892.2680.5910.74314.3

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 REPLACEMENTTHROUGHOUT3ELL1.3539.842753219299.820.15750.15580.1922RANDOM25.636
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]
-1.522.22-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.113
r_dihedral_angle_4_deg21.051
r_dihedral_angle_3_deg11.488
r_dihedral_angle_1_deg6.259
r_rigid_bond_restr1.57
r_angle_other_deg1.502
r_angle_refined_deg1.433
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.113
r_dihedral_angle_4_deg21.051
r_dihedral_angle_3_deg11.488
r_dihedral_angle_1_deg6.259
r_rigid_bond_restr1.57
r_angle_other_deg1.502
r_angle_refined_deg1.433
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms120
Heterogen Atoms55

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing