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Leishmania major Pteridine reductase 1 (PTR1) in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution: 12.5 mg/mL in 20 mM Sodium Acetate pH5.3 and 10 mM DTT.
Crystallisation buffer: 12% PEG 4600, 100 mM Sodium Acetate buffer pH 5.5 and 120-160 mM Calcium Acetate
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.699 α = 90 b = 104.25 β = 90 c = 137.04 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 PIXEL DECTRIS PILATUS 6M-F 2014-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.35 94.7 95.3 0.129 7.5 3.4 54151 2 17.2
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 2.35 2.48 97.1 0.431 2.7 3.3
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 2BFA 2.35 82.97 51393 2714 94.61 0.16574 0.16303 0.1662 0.2178 0.2193 RANDOM 24.154
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] -0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.979 r_dihedral_angle_4_deg 18.159 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 6.765 r_long_range_B_refined 6.18 r_mcangle_it 3.481 r_scbond_it 2.492 r_mcbond_it 2.162 r_angle_refined_deg 1.878 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.979 r_dihedral_angle_4_deg 18.159 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 6.765 r_long_range_B_refined 6.18 r_mcangle_it 3.481 r_scbond_it 2.492 r_mcbond_it 2.162 r_angle_refined_deg 1.878 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 7588 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing