6AY0

Crystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (PHM) soaked with peptide


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
1.9837.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.808α = 90
b = 66.532β = 90
c = 70.217γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-12-02MSINGLE 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)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
12.55094.50.0630.0690.02819.96.29437
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)
12.52.54690.1290.1420.0570.9885.5

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 REPLACEMENTTHROUGHOUT1PHM2.648.3815340796.130.19530.19170.2658RANDOM37.254
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]
-1.052.92-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg23.933
r_dihedral_angle_3_deg18.812
r_dihedral_angle_1_deg8.487
r_angle_refined_deg1.812
r_angle_other_deg1.055
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg23.933
r_dihedral_angle_3_deg18.812
r_dihedral_angle_1_deg8.487
r_angle_refined_deg1.812
r_angle_other_deg1.055
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2403
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
REFMACmodel building