6NCK

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6AO6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529319-24% PEG 4000, Tris HCl
Crystal Properties
Matthews coefficientSolvent content
1.9637.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.31α = 90
b = 65.88β = 90
c = 69.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9184NSLS-II17-ID-1

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.744.0899.60.130.1450.9918.194.873787253.452
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7799.10.6060.6920.8152.684.054

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 REPLACEMENTTHROUGHOUT6AO62.744.08747739499.570.22330.21960.2949RANDOM54.282
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]
-2.877.85-4.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.074
r_dihedral_angle_4_deg23.021
r_dihedral_angle_3_deg17.9
r_dihedral_angle_1_deg6.513
r_angle_refined_deg1.541
r_angle_other_deg1.346
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.074
r_dihedral_angle_4_deg23.021
r_dihedral_angle_3_deg17.9
r_dihedral_angle_1_deg6.513
r_angle_refined_deg1.541
r_angle_other_deg1.346
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2350
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction