6AN3

Crystal structure of H172A-peptidylglycine alpha-hydroxylating monooxygenase (PHM) mutant soaked with peptide (no CuH bound, no peptide bound)


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
238.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.029α = 90
b = 66.847β = 90
c = 70.246γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-10-05MSINGLE 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
12.055095.60.0510.0550.02220.85.417232
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)
12.052.0970.60.1450.1860.1140.9552

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 REPLACEMENTTHROUGHOUT1PHM2.0548.431629785895.430.20110.19690.2817RANDOM34.78
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]
-0.51.38-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.369
r_dihedral_angle_4_deg18.217
r_dihedral_angle_3_deg17.12
r_dihedral_angle_1_deg8.033
r_angle_refined_deg1.874
r_angle_other_deg1.084
r_chiral_restr0.121
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.369
r_dihedral_angle_4_deg18.217
r_dihedral_angle_3_deg17.12
r_dihedral_angle_1_deg8.033
r_angle_refined_deg1.874
r_angle_other_deg1.084
r_chiral_restr0.121
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2375
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms8

Software

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