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The crystal structure of a domain of protein VP0806 (unknown function) from Vibrio parahaemolyticus RIMD 2210633
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 20% PEG 8000, 0.1M MES, 0.2M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.001 α = 90 b = 116.476 β = 88.75 c = 62.224 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 2007-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918, 0.97938 APS 19-BM
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 2.14 29.12 95.5 0.059 28.23 3.4 19762 19762 45.1
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 2.14 2.2 77.3 0.378 2.47 2.9 1053
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.14 29.12 18728 18728 1011 95.04 0.22651 0.22651 0.22343 0.22 0.27922 0.2786 RANDOM 57.175
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] 1.14 -0.12 -1.62 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.574 r_dihedral_angle_3_deg 21.889 r_dihedral_angle_4_deg 11.561 r_dihedral_angle_1_deg 6.685 r_scangle_it 4.501 r_scbond_it 2.994 r_angle_refined_deg 2.073 r_mcangle_it 1.686 r_mcbond_it 0.995 r_symmetry_hbond_refined 0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.574 r_dihedral_angle_3_deg 21.889 r_dihedral_angle_4_deg 11.561 r_dihedral_angle_1_deg 6.685 r_scangle_it 4.501 r_scbond_it 2.994 r_angle_refined_deg 2.073 r_mcangle_it 1.686 r_mcbond_it 0.995 r_symmetry_hbond_refined 0.385 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 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 2712 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing DM phasing HKL-3000 phasing