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Crystal structure OF SCP1 phosphatase D98A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.5M ammonium sulfate, 0.2M lithium sulfate, 100MM HEPES 7.0. Crystal is then transferred to 100MM sodium citrate PH 5.5, 30% PEG8000, 20MM PNPP, 10MM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.791 α = 90 b = 78.979 β = 112.79 c = 62.939 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 2006-05-24 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 2.3 65.09 90.2 0.072 17.5 3.4 22230
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) 2.3 2.38 57.2 0.205 3.4 2.6
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 2GHQ 2.3 48.98 22230 1131 89.8 0.194 0.192 0.1855 0.231 0.2151 RANDOM 28.75
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] 0.4 1.28 1.23 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.876 r_dihedral_angle_4_deg 22.251 r_dihedral_angle_3_deg 17.269 r_dihedral_angle_1_deg 6.02 r_scangle_it 2.837 r_scbond_it 1.763 r_angle_refined_deg 1.35 r_mcangle_it 1.203 r_mcbond_it 0.672 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.876 r_dihedral_angle_4_deg 22.251 r_dihedral_angle_3_deg 17.269 r_dihedral_angle_1_deg 6.02 r_scangle_it 2.837 r_scbond_it 1.763 r_angle_refined_deg 1.35 r_mcangle_it 1.203 r_mcbond_it 0.672 r_nbtor_refined 0.307 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.087 r_metal_ion_refined 0.045 r_bond_refined_d 0.011 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 160 Heterogen Atoms 2
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling