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Crystal structure of Chlamydomonas reinhardtii prolyl-4 hydroxylase type I complexed with zinc and pyridine-2,4-dicarboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V4A PDB ENTRY 2V4A
Crystallization Crystal Properties Matthews coefficient Solvent content 1.8 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.92 α = 90 b = 60.25 β = 90 c = 116.85 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2006-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 32 98.1 0.1 6.3 2.3 152984 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 89.2 0.32 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V4A 1.85 29.17 33301 1753 99 0.186 0.183 0.1838 0.238 0.2364 RANDOM 23.2
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] 0.47 0.15 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.804 r_dihedral_angle_4_deg 19.433 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 5.895 r_scangle_it 2.535 r_scbond_it 1.667 r_angle_refined_deg 1.241 r_mcangle_it 1.066 r_mcbond_it 0.698 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.804 r_dihedral_angle_4_deg 19.433 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 5.895 r_scangle_it 2.535 r_scbond_it 1.667 r_angle_refined_deg 1.241 r_mcangle_it 1.066 r_mcbond_it 0.698 r_nbtor_refined 0.303 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_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 Atoms Number Protein Atoms 3225 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing