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Crystal Structure of Human Pyridoxal Phosphate Phosphatase with Mg2+ at 1.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YOC PDB entry 2YOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 100mM Tris-HCl pH 8.5, 17% PEG 20000, 100mM Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.245 α = 90 b = 54.245 β = 90 c = 213.182 γ = 90
Symmetry Space Group P 43 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 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97900 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 1.9 50 100 0.068 0.052 9.5 8.3 26274 26274
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) 1.9 1.97 100 0.624 8.2 4819
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 PDB entry 2YOC 1.9 48.34 26182 26182 1332 99.98 0.213 0.213 0.211 0.2084 0.25 0.2508 RANDOM 32.203
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] 0.29 0.29 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.997 r_dihedral_angle_4_deg 17.508 r_dihedral_angle_3_deg 15.049 r_dihedral_angle_1_deg 7.347 r_scangle_it 3.453 r_scbond_it 2.199 r_mcangle_it 1.538 r_angle_refined_deg 1.454 r_mcbond_it 0.906 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.997 r_dihedral_angle_4_deg 17.508 r_dihedral_angle_3_deg 15.049 r_dihedral_angle_1_deg 7.347 r_scangle_it 3.453 r_scbond_it 2.199 r_mcangle_it 1.538 r_angle_refined_deg 1.454 r_mcbond_it 0.906 r_nbtor_refined 0.3 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.143 r_symmetry_vdw_refined 0.13 r_chiral_restr 0.088 r_metal_ion_refined 0.022 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing