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Crystal structure of the PPM Ser-Thr phosphatase MsPP from Mycobacterium smegmatis in complex with cacodylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CM1 PDB ENTRY 2CM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 18% PEG12K, 85 MM NA CACODYLATE PH 6.5, 120 MM NA ACETATE, 13% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.7 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.568 α = 90 b = 65.786 β = 90 c = 110.059 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2005-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.45 25.9 99 0.05 15.6 3.8 47486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 97.7 0.43 2.6 3.7
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 2CM1 1.45 25.38 45070 2355 98.9 0.179 0.178 0.1756 0.191 0.1885 RANDOM 19.59
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] -0.08 0.74 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 20.961 r_dihedral_angle_3_deg 12.767 r_dihedral_angle_1_deg 5.718 r_scangle_it 3.859 r_scbond_it 2.435 r_mcangle_it 1.497 r_angle_refined_deg 1.459 r_mcbond_it 0.995 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 20.961 r_dihedral_angle_3_deg 12.767 r_dihedral_angle_1_deg 5.718 r_scangle_it 3.859 r_scbond_it 2.435 r_mcangle_it 1.497 r_angle_refined_deg 1.459 r_mcbond_it 0.995 r_nbtor_refined 0.304 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.095 r_bond_refined_d 0.013 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 1694 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing