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Algal prolyl 4-hydroxylase complexed with zinc and (Ser-Pro)5 peptide substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V4A PDB ENTRY 2V4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under-oil 5.5 295 5% PEG Smear, 0.1M acetate, 10mM zinc acetate, pH 5.5, Microbatch under-oil, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.25 α = 90 b = 58.75 β = 102.21 c = 105.16 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2007-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.932 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 1.98 25 93.4 0.062 12.16 2.9 75581 68688 24.62
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 1.98 2.04 87.1 0.201 4.3 2.5 4412
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1.98 20.6 68677 65243 3434 93.45 0.21888 0.21704 0.2195 0.25392 0.2543 RANDOM 11.741
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] -0.07 1.98 -0.2 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.487 r_dihedral_angle_4_deg 24.418 r_dihedral_angle_3_deg 16.734 r_dihedral_angle_1_deg 6.514 r_scangle_it 3.327 r_scbond_it 2.289 r_angle_other_deg 2.263 r_angle_refined_deg 1.813 r_mcangle_it 1.393 r_mcbond_it 0.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.487 r_dihedral_angle_4_deg 24.418 r_dihedral_angle_3_deg 16.734 r_dihedral_angle_1_deg 6.514 r_scangle_it 3.327 r_scbond_it 2.289 r_angle_other_deg 2.263 r_angle_refined_deg 1.813 r_mcangle_it 1.393 r_mcbond_it 0.852 r_mcbond_other 0.242 r_chiral_restr 0.101 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6345 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 34
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction