5WKW

Crystal structure of apo wild type peptidylglycine alpha-hydroxylating monooxygenase (PHM)


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
Crystal Properties
Matthews coefficientSolvent content
1.9737.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.726α = 90
b = 66.568β = 90
c = 70.186γ = 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)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
11.795099.10.07814.87.426454
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)
11.791.82920.3874.2

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdbid XX1.7948.324960132598.560.210.20660.2735RANDOM28.691
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]
-0.340.56-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.336
r_dihedral_angle_4_deg19.265
r_dihedral_angle_3_deg15.352
r_dihedral_angle_1_deg7.366
r_angle_refined_deg1.81
r_angle_other_deg1.043
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.336
r_dihedral_angle_4_deg19.265
r_dihedral_angle_3_deg15.352
r_dihedral_angle_1_deg7.366
r_angle_refined_deg1.81
r_angle_other_deg1.043
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2433
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms13

Software

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