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Crystal structure of Phosphoserine phosphatase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 289.15 0.1 M phosphate citrate buffer, pH 4.2, 4% PEG 300
Crystal Properties Matthews coefficient Solvent content 3 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.172 α = 90 b = 109.172 β = 90 c = 165.911 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE RIGAKU RAXIS IV 2015-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 94.55 98.7 0.996 27.6 14.6 39785
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.802 3.4 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4IJ5 2 94.55 37779 1948 98.71 0.16823 0.16657 0.1783 0.20193 0.2152 RANDOM 32.077
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] -0.52 -0.26 -0.52 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.912 r_dihedral_angle_4_deg 22.327 r_dihedral_angle_3_deg 13.129 r_long_range_B_other 8.283 r_long_range_B_refined 8.28 r_scangle_other 7.036 r_dihedral_angle_1_deg 6.359 r_scbond_it 4.873 r_scbond_other 4.873 r_mcangle_it 3.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.912 r_dihedral_angle_4_deg 22.327 r_dihedral_angle_3_deg 13.129 r_long_range_B_other 8.283 r_long_range_B_refined 8.28 r_scangle_other 7.036 r_dihedral_angle_1_deg 6.359 r_scbond_it 4.873 r_scbond_other 4.873 r_mcangle_it 3.912 r_mcangle_other 3.912 r_angle_other_deg 3.685 r_mcbond_it 2.864 r_mcbond_other 2.862 r_angle_refined_deg 2.166 r_chiral_restr 0.138 r_bond_refined_d 0.022 r_gen_planes_other 0.022 r_gen_planes_refined 0.012 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3049 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing