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Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis bound to cobalt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JSW PDB entry 1jsw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 46.3 mg/mL BrabA.00047.a.A6 PS00513 against JCSG+ condition G3, 10 mM CoCl2, 0.1 M Tris, 20% polyvinyl pyrrolidone K15 with 20% ethylene glycol as cryo-protectant, crsytal tracking ID 215219g3, 3C protease cleaved, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.33 α = 90 b = 113.55 β = 90 c = 236.86 γ = 90
Symmetry Space Group P 21 21 21
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 2010-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.58 50 99.1 0.146 10.03 7.1 81644 80944 -3 29.903
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) 2.58 2.65 99 0.565 3.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1jsw 2.58 50 80691 4054 98.85 0.1984 0.1959 0.2454 0.2166 RANDOM 29.6871
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] -1.65 -0.06 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.22 r_dihedral_angle_3_deg 18.128 r_dihedral_angle_4_deg 17.4 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.558 r_scbond_it 1.999 r_angle_refined_deg 1.538 r_mcangle_it 1.227 r_mcbond_it 0.624 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.22 r_dihedral_angle_3_deg 18.128 r_dihedral_angle_4_deg 17.4 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.558 r_scbond_it 1.999 r_angle_refined_deg 1.538 r_mcangle_it 1.227 r_mcbond_it 0.624 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13775 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 20
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction