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Crystal structure of human purine nucleoside phosphorylase mutant H257G with Imm-H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.17 α = 90 b = 142.17 β = 90 c = 168.674 γ = 120
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 QUANTUM 315 2006-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.100 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.59 30 97.2 0.079 0.069 9.4 6.5 20553 19978 63.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.69 75.8 0.437 0.437 1.6 2.8 1543
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1RR6 2.59 8 19832 19238 994 97 0.197 0.197 0.194 0.2023 0.243 0.2434 RANDOM 56.926
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_3_deg 20.742 r_dihedral_angle_4_deg 20.706 r_dihedral_angle_1_deg 8.252 r_scangle_it 4.692 r_scbond_it 3.06 r_mcangle_it 2.286 r_angle_refined_deg 2.246 r_mcbond_it 1.34 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_3_deg 20.742 r_dihedral_angle_4_deg 20.706 r_dihedral_angle_1_deg 8.252 r_scangle_it 4.692 r_scbond_it 3.06 r_mcangle_it 2.286 r_angle_refined_deg 2.246 r_mcbond_it 1.34 r_nbtor_refined 0.324 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.05 r_bond_refined_d 0.024 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2176 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction