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Crystal structure of LacB from Trametes sp. AH28-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GYC PDB ENTRY 1gyc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 283 0.1M Sodium citrate tribasic dihydrate (pH 5.2), 25% PEG 4000, 10% iso-propanol , VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.39 63.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.778 α = 90 b = 98.778 β = 90 c = 149.96 γ = 90
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 MAR CCD 165 mm 2008-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.1000 BSRF 3W1A
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 3.4 150.8 5.3 19312 17991 8
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 3.44 3.55
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 (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 PDB ENTRY 1gyc 3.44 30 19312 17991 976 98.92 0.22634 0.22301 0.2231 0.29165 0.291 RANDOM 50.625
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] 2.49 2.49 -4.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.891 r_dihedral_angle_4_deg 17.95 r_dihedral_angle_3_deg 16.335 r_dihedral_angle_1_deg 5.594 r_scangle_it 2.566 r_scbond_it 1.722 r_angle_refined_deg 1.504 r_mcangle_it 1.311 r_mcbond_it 0.764 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.891 r_dihedral_angle_4_deg 17.95 r_dihedral_angle_3_deg 16.335 r_dihedral_angle_1_deg 5.594 r_scangle_it 2.566 r_scbond_it 1.722 r_angle_refined_deg 1.504 r_mcangle_it 1.311 r_mcbond_it 0.764 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.219 r_metal_ion_refined 0.166 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_symmetry_hbond_refined 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7617 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement