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Leishmania major pteridine reductase 1 in complex with NADP and CB3717
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E92 PDB ENTRY 1E92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 15 MG/ML PROTEIN, 0.1M NAAC/HAC BUFFER PH 5.5, 10% MPEG 5000, 0.065M CAAC2, 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.538 α = 90 b = 103.834 β = 90 c = 137.045 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.7 30 92.7 0.14 9.8 3.9 35456 37.4
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 2.7 2.8 85 0.41 2.9
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 1E92 2.7 24.5 33423 1764 100 0.205 0.203 0.2034 0.236 0.2379 RANDOM 28.92
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] -0.46 0.86 -0.4
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.686 r_dihedral_angle_1_deg 2.98 r_scbond_it 2.24 r_mcangle_it 1.697 r_angle_refined_deg 0.987 r_mcbond_it 0.828 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.147
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.686 r_dihedral_angle_1_deg 2.98 r_scbond_it 2.24 r_mcangle_it 1.697 r_angle_refined_deg 0.987 r_mcbond_it 0.828 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 7752 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 356
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing