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Crystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 30% MPD, 0.1M HEPES, 0.2M Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.48 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.49 α = 90 b = 80.49 β = 90 c = 207.05 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 87 CCD ADSC QUANTAM Q315 MIRRORS 2005-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.989 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 20 92.3 0.122 0.118 6.7 9.2 33912 32826 0.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 79.6 0.191 0.222 2.1 4.4 2765
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 SAD THROUGHOUT 2.2 103.69 32826 31792 1017 92.35 0.247 0.23725 0.23489 0.2382 0.30788 0.3074 RANDOM 27.415
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] -0.52 -0.52 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.827 r_dihedral_angle_4_deg 20.552 r_dihedral_angle_3_deg 19.65 r_scangle_it 11.064 r_dihedral_angle_1_deg 8.48 r_scbond_it 7.583 r_angle_refined_deg 1.397 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.234 r_mcangle_it 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.827 r_dihedral_angle_4_deg 20.552 r_dihedral_angle_3_deg 19.65 r_scangle_it 11.064 r_dihedral_angle_1_deg 8.48 r_scbond_it 7.583 r_angle_refined_deg 1.397 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.234 r_mcangle_it 0.218 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.19 r_mcbond_it 0.131 r_chiral_restr 0.117 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4264 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction HKL-2000 data reduction SOLVE phasing RESOLVE model building REFMAC refinement SCALEPACK data scaling RESOLVE phasing