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Crystal structure of SCP1 phosphatase D206A mutant with trapped inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GHQ pdb entry 2GHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.5M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 100MM HEPES, pH 7.0. CRYSTAL TRANSFERRED TO 100MM MES, pH 6.5, 30% PEG8000, 20MM PNPP, AND 0.2M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.36 63.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.508 α = 90 b = 77.256 β = 112.52 c = 63.116 γ = 90
Symmetry Space Group C 1 2 1
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 MIRRORS 2006-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 48.62 95 0.075 13.4 3.3 17693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.45 2.54 53.2 0.227 2.1 2.1
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 pdb entry 2GHQ 2.45 39.25 17693 864 95.1 0.207 0.205 0.1929 0.254 0.2425 RANDOM 37.48
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] -0.13 1.45 0.59 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.009 r_dihedral_angle_4_deg 24.699 r_dihedral_angle_3_deg 18.365 r_dihedral_angle_1_deg 6.853 r_scangle_it 3.152 r_scbond_it 1.965 r_angle_refined_deg 1.603 r_mcangle_it 1.312 r_mcbond_it 0.727 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.009 r_dihedral_angle_4_deg 24.699 r_dihedral_angle_3_deg 18.365 r_dihedral_angle_1_deg 6.853 r_scangle_it 3.152 r_scbond_it 1.965 r_angle_refined_deg 1.603 r_mcangle_it 1.312 r_mcbond_it 0.727 r_nbtor_refined 0.315 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.216 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.104 r_symmetry_hbond_refined 0.103 r_metal_ion_refined 0.035 r_bond_refined_d 0.014 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2902 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 12
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling