5WJA

Crystal structure of H107A peptidylglycine alpha-hydroxylating monooxygenase (PHM) in complex with citrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PHM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.529319-24% PEG 4000, Tris HCL, citrate
Crystal Properties
Matthews coefficientSolvent content
2.1943.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.544α = 90
b = 100.613β = 90
c = 101.582γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

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
12.329.7799.60.0480.0690.0480.9969.61.927694
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)
12.32.3896.30.3390.4790.3390.8281.9

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 REPLACEMENTTHROUGHOUT1PHM2.329.7726271139099.570.20170.19790.2732RANDOM51.392
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]
4.6-3.16-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.071
r_dihedral_angle_3_deg17.593
r_dihedral_angle_4_deg14.979
r_dihedral_angle_1_deg8.883
r_angle_refined_deg1.78
r_angle_other_deg1.053
r_chiral_restr0.136
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.071
r_dihedral_angle_3_deg17.593
r_dihedral_angle_4_deg14.979
r_dihedral_angle_1_deg8.883
r_angle_refined_deg1.78
r_angle_other_deg1.053
r_chiral_restr0.136
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4798
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing