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Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 277 9.975% PEG MME 5000, 0.05M Acetic Acid, 0.052M Citrate_Na3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.287 α = 90 b = 103.553 β = 90 c = 57.27 γ = 90
Symmetry Space Group P 21 21 2
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 2003-10-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9802, 1.0000 ALS 8.2.2
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 2.3 49.629 99.1 0.076 0.076 5.7 3.4 26695
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 2.3 2.36 91.6 0.384 0.384 2 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.3 49.61 26666 1345 98.98 0.201 0.198 0.2038 0.252 0.2558 RANDOM 37.389
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] -3.03 2.14 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.11 r_dihedral_angle_4_deg 17.118 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 6.225 r_scangle_it 5.296 r_scbond_it 3.819 r_mcangle_it 2.081 r_mcbond_it 1.599 r_angle_refined_deg 1.225 r_angle_other_deg 0.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.11 r_dihedral_angle_4_deg 17.118 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 6.225 r_scangle_it 5.296 r_scbond_it 3.819 r_mcangle_it 2.081 r_mcbond_it 1.599 r_angle_refined_deg 1.225 r_angle_other_deg 0.768 r_mcbond_other 0.377 r_nbd_other 0.175 r_nbtor_refined 0.171 r_nbd_refined 0.17 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_other 0.154 r_symmetry_hbond_refined 0.152 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4171 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SOLVE phasing