6ALV

Crystal structure of H107A-peptidylglycine alpha-hydroxylating monooxygenase (PHM) mutant (no CuH 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, 0.54 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.7955.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.045α = 90
b = 68.857β = 90
c = 81.532γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-02-06MSINGLE 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
13.55092.20.10283.64848
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.5688.92.7

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 REPLACEMENTTHROUGHOUT1PHM3.550434322787.280.27610.2750.2978RANDOM45.043
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]
0.26-1.441.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.87
r_dihedral_angle_3_deg21.292
r_dihedral_angle_4_deg20.027
r_dihedral_angle_1_deg8.883
r_angle_refined_deg1.738
r_angle_other_deg1.075
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.87
r_dihedral_angle_3_deg21.292
r_dihedral_angle_4_deg20.027
r_dihedral_angle_1_deg8.883
r_angle_refined_deg1.738
r_angle_other_deg1.075
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2372
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms29

Software

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