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Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 500mM NaCl, 10mM HEPES, 4%(v/v) Tacsimate, 18%(w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.33 α = 90 b = 96.34 β = 90 c = 333.26 γ = 90
Symmetry Space Group P 2 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 MAR225HE 2010-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 30 100 111393 111393 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 1.9 3.5
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 2PMB 2.1 29.74 110924 105372 5551 99.95 0.20941 0.20635 0.2058 0.26674 0.2654 RANDOM 33.972
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] 0.31 -0.07 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 22.183 r_dihedral_angle_3_deg 17.542 r_long_range_B_refined 7.417 r_dihedral_angle_1_deg 7.232 r_mcangle_it 5.243 r_scbond_it 4.473 r_mcbond_it 3.875 r_angle_refined_deg 2.234 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 22.183 r_dihedral_angle_3_deg 17.542 r_long_range_B_refined 7.417 r_dihedral_angle_1_deg 7.232 r_mcangle_it 5.243 r_scbond_it 4.473 r_mcbond_it 3.875 r_angle_refined_deg 2.234 r_chiral_restr 0.158 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 12536 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling