5WM0

Crystal structure of apo wild type peptidylglycine alpha-hydroxylating monooxygenase (PHM) soaked with peptide (peptide not observed)


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 Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.099α = 90
b = 65.93β = 90
c = 69.809γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2016-11-28MSINGLE 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
12.45099.20.0750.0820.03415.25.511068
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)
12.42.4488.10.3290.4050.2320.8432.6

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 SYNTHESISTHROUGHOUT1PHM2.447.931046856299.070.20390.19970.2811RANDOM51.291
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]
-1.152.73-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.875
r_dihedral_angle_3_deg19.311
r_dihedral_angle_4_deg17.556
r_dihedral_angle_1_deg8.658
r_angle_refined_deg1.933
r_angle_other_deg1.129
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.875
r_dihedral_angle_3_deg19.311
r_dihedral_angle_4_deg17.556
r_dihedral_angle_1_deg8.658
r_angle_refined_deg1.933
r_angle_other_deg1.129
r_chiral_restr0.116
r_bond_refined_d0.017
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 Atoms2413
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACphasing