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Crystal structure of human pterin-4-alpha-carbinolamine dehydratase 2 (PCBD2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RU0 PDB ENTRY 1RU0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.4 SODIUM MALONATE
Crystal Properties Matthews coefficient Solvent content 2.51 50.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.547 α = 90 b = 94.044 β = 90 c = 48.33 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.45 48.33 100 0.05 18.1 6.5 21250 2
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 1.45 1.48 100 0.76 2.7 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RU0 1.45 48.33 20155 1090 99.96 0.14507 0.14389 0.167 0.1792 RANDOM 22.597
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] -0.36 -1.21 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.24 r_sphericity_free 28.852 r_dihedral_angle_3_deg 11.814 r_dihedral_angle_4_deg 11.211 r_sphericity_bonded 8.508 r_dihedral_angle_1_deg 6.403 r_rigid_bond_restr 5.168 r_scbond_it 3.041 r_mcangle_it 2.785 r_mcbond_it 2.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.24 r_sphericity_free 28.852 r_dihedral_angle_3_deg 11.814 r_dihedral_angle_4_deg 11.211 r_sphericity_bonded 8.508 r_dihedral_angle_1_deg 6.403 r_rigid_bond_restr 5.168 r_scbond_it 3.041 r_mcangle_it 2.785 r_mcbond_it 2.563 r_mcbond_other 2.415 r_angle_refined_deg 1.427 r_angle_other_deg 0.811 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 792 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing