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Crystal structure of probable yrbi family phosphatase from pseudomonas syringae pv.phaseolica 1448a complexed with magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 100MM TRIS-HCL, PH 7.0, 30% PEG 3K, 200MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.11 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.302 α = 90 b = 126.733 β = 95.57 c = 106.531 γ = 90
Symmetry Space Group P 1 21 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 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.88 40 95.6 0.064 6.5 2 163907 -5 32.512
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) 1.88 1.91 71.9 0.9 0.95 1.7
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 MR THROUGHOUT 3MN1 1.9 40 150181 4674 97.84 0.18112 0.17931 0.18 0.24038 0.2389 RANDOM 52.477
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] -0.35 3.29 -4.8 5.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.959 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 14.923 r_scangle_it 10.027 r_scbond_it 6.76 r_mcangle_it 5.272 r_dihedral_angle_1_deg 4.98 r_mcbond_it 3.798 r_angle_refined_deg 1.144 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.959 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 14.923 r_scangle_it 10.027 r_scbond_it 6.76 r_mcangle_it 5.272 r_dihedral_angle_1_deg 4.98 r_mcbond_it 3.798 r_angle_refined_deg 1.144 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15822 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 89
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling