7E07

Trans-3/4-proline-hydroxylase H11 with AKG and L-proline


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289.150.7M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
3.4264.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.437α = 90
b = 106.437β = 90
c = 145.016γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979SSRFBL17U

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
12.1485.8194.460.1320.1350.0258.328.644086
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)
12.142.18990.5290.5380.10.9811.328.9

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 REPLACEMENTTHROUGHOUT6LNS2.1485.8141919216794.460.19070.18850.2332RANDOM39
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]
1.691.69-3.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.033
r_dihedral_angle_4_deg19.134
r_dihedral_angle_3_deg17.001
r_dihedral_angle_1_deg7.503
r_angle_refined_deg1.963
r_angle_other_deg1.096
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.033
r_dihedral_angle_4_deg19.134
r_dihedral_angle_3_deg17.001
r_dihedral_angle_1_deg7.503
r_angle_refined_deg1.963
r_angle_other_deg1.096
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4218
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing