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Crystal structure of wild type peptide-binding domain of human type I collagen prolyl 4-hydroxylase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJC PDB ENTRY 1TJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.5 PROTEIN WAS CRYSTALLIZED FROM 1 M NA CITRATE, 100 MM CHES, PH 9.5.
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.472 α = 90 b = 59.046 β = 90 c = 61.668 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 MIRRORS 2005-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.03 42.6 98.8 0.05 21 5.6 9304
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 2.03 2.14 93.2 0.16 10.1 3.4
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 1TJC 2.03 42.65 8227 432 93.3 0.199 0.196 0.2172 0.265 0.2753 RANDOM 14.28
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] -0.27 -0.75 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_3_deg 17.474 r_dihedral_angle_1_deg 14.725 r_dihedral_angle_4_deg 4.693 r_scangle_it 4.579 r_mcangle_it 3.947 r_scbond_it 3.391 r_mcbond_it 2.921 r_angle_other_deg 2.013 r_angle_refined_deg 1.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_3_deg 17.474 r_dihedral_angle_1_deg 14.725 r_dihedral_angle_4_deg 4.693 r_scangle_it 4.579 r_mcangle_it 3.947 r_scbond_it 3.391 r_mcbond_it 2.921 r_angle_other_deg 2.013 r_angle_refined_deg 1.497 r_symmetry_vdw_refined 0.341 r_symmetry_vdw_other 0.303 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.089 r_nbd_other 0.075 r_nbd_refined 0.061 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 859 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing