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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C7V PDB ENTRY 2C7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.966 α = 90 b = 87.64 β = 115.75 c = 84.074 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944 HG 2012-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.9 43.82 95 0.07 16.3 3.7 72202
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 1.9 2 81.9 0.4 3.2 3.2
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 2C7V 1.9 43.82 68466 3672 94.66 0.15409 0.1515 0.164 0.20241 0.2114 RANDOM 22.706
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] -0.95 -0.19 2.74 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 17.989 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 6.063 r_mcangle_it 2.709 r_scbond_it 2.296 r_angle_refined_deg 1.771 r_mcbond_it 1.77 r_mcbond_other 1.769 r_angle_other_deg 0.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 17.989 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 6.063 r_mcangle_it 2.709 r_scbond_it 2.296 r_angle_refined_deg 1.771 r_mcbond_it 1.77 r_mcbond_other 1.769 r_angle_other_deg 0.935 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7417 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing