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N-phenylglycinonitrile in complex with T4 lysozyme L99A/M102Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 277 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.131 α = 90 b = 60.131 β = 90 c = 96.886 γ = 120
Symmetry Space Group P 32 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 110 CCD ADSC QUANTUM 315 Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) 2006-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979462 SSRL BL9-1
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 1.29 52.06 98.8 0.08 10 6.6 51136 51136
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) 1.29 1.34 100 0.569 7 5120
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1LGU 1.29 52.06 51074 51074 2600 98.76 0.179 0.179 0.178 0.191 0.2052 RANDOM 14.879
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 13.18 r_dihedral_angle_3_deg 11.153 r_dihedral_angle_1_deg 4.768 r_scangle_it 2.479 r_sphericity_free 2.393 r_scbond_it 2.388 r_rigid_bond_restr 2.312 r_sphericity_bonded 2.057 r_angle_refined_deg 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_4_deg 13.18 r_dihedral_angle_3_deg 11.153 r_dihedral_angle_1_deg 4.768 r_scangle_it 2.479 r_sphericity_free 2.393 r_scbond_it 2.388 r_rigid_bond_restr 2.312 r_sphericity_bonded 2.057 r_angle_refined_deg 1.071 r_mcangle_it 1.007 r_mcbond_it 0.806 r_nbtor_refined 0.307 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1329 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection REFMAC phasing