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Crystal structure of Lipk107
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 Sodium citrate, PEG4000,2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.484 α = 90 b = 65.484 β = 90 c = 63.871 γ = 120
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 315r 2010-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 56.7 95 20690 19653 2 2
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 2.03 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT 1EX9 2 50 2 20690 19653 1065 99.8 0.1824 0.18124 0.17941 0.1462 0.21473 0.158 RANDOM 18.536
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] -0.42 -0.21 -0.42 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.947 r_dihedral_angle_4_deg 19.821 r_dihedral_angle_3_deg 13.696 r_dihedral_angle_1_deg 5.251 r_scangle_it 2.062 r_scbond_it 1.381 r_angle_refined_deg 1.049 r_mcangle_it 0.788 r_mcbond_it 0.483 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.947 r_dihedral_angle_4_deg 19.821 r_dihedral_angle_3_deg 13.696 r_dihedral_angle_1_deg 5.251 r_scangle_it 2.062 r_scbond_it 1.381 r_angle_refined_deg 1.049 r_mcangle_it 0.788 r_mcbond_it 0.483 r_nbtor_refined 0.304 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2137 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling