☰ Navigation Tabs
Crystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 1.0000M LiCl, 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.56 α = 90 b = 68.45 β = 90 c = 107.46 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-11-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97864,0.97817 SSRL BL11-1
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 27.973 97.7 0.025 16.47 63677 -3 18.269
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 1.5 88.8 0.374 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.45 27.973 63622 3217 99.39 0.149 0.148 0.1547 0.167 0.1711 RANDOM 20.701
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] 0.61 -0.46 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.429 r_dihedral_angle_4_deg 13.977 r_dihedral_angle_3_deg 10.327 r_dihedral_angle_1_deg 4.535 r_scangle_it 2.631 r_mcangle_it 1.911 r_scbond_it 1.7 r_angle_refined_deg 1.664 r_mcbond_it 1.421 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.429 r_dihedral_angle_4_deg 13.977 r_dihedral_angle_3_deg 10.327 r_dihedral_angle_1_deg 4.535 r_scangle_it 2.631 r_mcangle_it 1.911 r_scbond_it 1.7 r_angle_refined_deg 1.664 r_mcbond_it 1.421 r_angle_other_deg 0.926 r_mcbond_other 0.344 r_symmetry_vdw_other 0.309 r_nbd_refined 0.226 r_nbd_other 0.214 r_symmetry_hbond_refined 0.197 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.096 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2400 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing