2JIJ

Crystal structure of the apo form of Chlamydomonas reinhardtii prolyl- 4 hydroxylase type I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V4APDB ENTRY 2V4A

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.32α = 90
b = 117.46β = 90
c = 72.04γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.93598.80.089.72691672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93990.451.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2V4A2.933.831789896098.80.2140.2120.261RANDOM39.42
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]
-0.30.76-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.624
r_dihedral_angle_4_deg18.872
r_dihedral_angle_3_deg17.474
r_dihedral_angle_1_deg9.57
r_angle_refined_deg1.705
r_scangle_it1.595
r_scbond_it1.025
r_mcangle_it0.855
r_mcbond_it0.49
r_symmetry_hbond_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.624
r_dihedral_angle_4_deg18.872
r_dihedral_angle_3_deg17.474
r_dihedral_angle_1_deg9.57
r_angle_refined_deg1.705
r_scangle_it1.595
r_scbond_it1.025
r_mcangle_it0.855
r_mcbond_it0.49
r_symmetry_hbond_refined0.318
r_nbtor_refined0.314
r_nbd_refined0.222
r_xyhbond_nbd_refined0.145
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4640
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing