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crystal structure of human pyridoxal 5'-phosphate phosphatase
Crystallization Crystal Properties Matthews coefficient Solvent content 2.47 49.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.3 α = 90 b = 54.3 β = 90 c = 213.9 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 2004-10-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B PAL/PLS 6B
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 2.3 20 94 0.08 14 3.4 25788 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 MAD THROUGHOUT 2.4 19.06 11651 630 92.4 0.206 0.203 0.2013 0.257 0.2511 RANDOM 25.32
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] 0.61 0.61 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.933 r_dihedral_angle_4_deg 20.558 r_dihedral_angle_3_deg 18.558 r_dihedral_angle_1_deg 6.303 r_scangle_it 3.082 r_scbond_it 1.983 r_angle_refined_deg 1.474 r_mcangle_it 1.396 r_mcbond_it 0.782 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.933 r_dihedral_angle_4_deg 20.558 r_dihedral_angle_3_deg 18.558 r_dihedral_angle_1_deg 6.303 r_scangle_it 3.082 r_scbond_it 1.983 r_angle_refined_deg 1.474 r_mcangle_it 1.396 r_mcbond_it 0.782 r_nbtor_refined 0.299 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2188 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement