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Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7 Ang resolution bound to molybdate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AMF PDB ENTRY 1AMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2M lithium sulfate, 0.1M Tris-HCl, 30% PEG 4000 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.05 40.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.153 α = 90 b = 172.138 β = 90 c = 112.036 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm mirror 2005-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.421 LNLS D03B-MX1
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 1.7 50 99.8 0.062 26.6 5.7 72786 72786
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) 1 1.7 1.76 99.3 0.415 3.3 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1AMF 1.7 30.07 72533 70345 2188 99.32 0.16833 0.16726 0.1761 0.20237 0.2063 RANDOM 25.879
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] 0.62 -0.03 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.647 r_dihedral_angle_4_deg 13.507 r_dihedral_angle_3_deg 12.613 r_dihedral_angle_1_deg 5.572 r_scangle_it 2.996 r_scbond_it 1.776 r_angle_refined_deg 1.752 r_mcangle_it 1.032 r_mcbond_it 0.657 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.647 r_dihedral_angle_4_deg 13.507 r_dihedral_angle_3_deg 12.613 r_dihedral_angle_1_deg 5.572 r_scangle_it 2.996 r_scbond_it 1.776 r_angle_refined_deg 1.752 r_mcangle_it 1.032 r_mcbond_it 0.657 r_nbtor_refined 0.327 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.096 r_bond_refined_d 0.012 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_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5139 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data scaling MOLREP phasing