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Crystal structure of human pyridoxal 5'-phosphate phosphatase with its substrate
Crystallization Crystal Properties Matthews coefficient Solvent content 2.24 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.303 α = 90 b = 54.303 β = 90 c = 210.19 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 CCD 2005-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 1.8 40 96 0.04 50 6.8 29341 2
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 (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 1.8 27.16 27818 1485 96.5 0.187 0.185 0.1841 0.226 0.2251 RANDOM 28.84
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.758 r_dihedral_angle_4_deg 15.369 r_dihedral_angle_3_deg 14.093 r_dihedral_angle_1_deg 5.763 r_scangle_it 4.16 r_scbond_it 2.627 r_mcangle_it 1.699 r_angle_refined_deg 1.526 r_mcbond_it 1.002 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.758 r_dihedral_angle_4_deg 15.369 r_dihedral_angle_3_deg 14.093 r_dihedral_angle_1_deg 5.763 r_scangle_it 4.16 r_scbond_it 2.627 r_mcangle_it 1.699 r_angle_refined_deg 1.526 r_mcbond_it 1.002 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 2187 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement