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1.00 A Structure of Lysozyme Crystallized with (R)-2-methyl-2,4- pentanediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other INHOUSE MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 CRYSTALLIZATION BY HANGING DROP AT 4C. CONDITIONS IN DROP: PROTEIN AT 35 MG/ML IN 200MM TRIS (PH 8.0) AND 60% V/V (R)-MPD. CONDITIONS IN RESERVOIR: 200MM TRIS (PH 8.0).
Crystal Properties Matthews coefficient Solvent content 2.03 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.53 α = 90 b = 77.53 β = 90 c = 37.895 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC CCD TOROIDAL FOCUSING MIRROR 2011-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 15 99.3 0.07 43.3 13.7 62397 2
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 1.02 99 0.82 2.51 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT INHOUSE MODEL 1 13.3 59136 3155 99.22 0.12463 0.12364 0.1412 0.14355 0.1566 RANDOM 11.238
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] -0.53 -0.53 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.616 r_sphericity_free 19.02 r_dihedral_angle_4_deg 14.1 r_dihedral_angle_3_deg 11.715 r_sphericity_bonded 6.962 r_dihedral_angle_1_deg 5.723 r_angle_refined_deg 1.306 r_rigid_bond_restr 1.203 r_angle_other_deg 0.938 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.616 r_sphericity_free 19.02 r_dihedral_angle_4_deg 14.1 r_dihedral_angle_3_deg 11.715 r_sphericity_bonded 6.962 r_dihedral_angle_1_deg 5.723 r_angle_refined_deg 1.306 r_rigid_bond_restr 1.203 r_angle_other_deg 0.938 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing