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Leishmania major pteridine reductase 1 in complex with NADPH
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, 12% MPEG 5000, 0.075M CAAC2, 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.308 α = 90 b = 103.493 β = 90 c = 137.977 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 ID14-2 ESRF ID14-2
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 2.6 25 96.8 0.09 13.6 3.7 40607 41.8
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 2.6 2.7 92.6 0.22 5.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E92 2.6 24.5 38452 2055 100 0.229 0.226 0.2295 0.269 0.2734 RANDOM 36.26
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] -1.73 0.92 0.8
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.002 r_dihedral_angle_1_deg 4.262 r_scbond_it 3.407 r_mcangle_it 2.275 r_angle_refined_deg 1.337 r_mcbond_it 1.187 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.122
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.002 r_dihedral_angle_1_deg 4.262 r_scbond_it 3.407 r_mcangle_it 2.275 r_angle_refined_deg 1.337 r_mcbond_it 1.187 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 7787 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing