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Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis in native form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OCE PDB entry 3OCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 86.6 mg/mL of BrabA.00047.a.A5 PS00511 full lenght tag against JCSG+ condition A9, 0.2 M ammonium chloride, 20% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 215952a9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.9 35.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.23 α = 90 b = 86.46 β = 91.91 c = 105.16 γ = 90
Symmetry Space Group P 1 21 1
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 2010-07-02 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 2.1 50 99.5 0.086 12.65 3.6 90194 89781 -3 30.177
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) 2.1 2.15 98.3 0.528 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 PDB entry 3OCE 2.1 50 89651 4501 99.41 0.174 0.1712 0.1756 0.2273 0.2288 RANDOM 32.2479
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] -1.45 -0.49 1.18 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 16.171 r_dihedral_angle_3_deg 14.183 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.631 r_scbond_it 2.262 r_angle_refined_deg 1.464 r_mcangle_it 1.259 r_mcbond_it 0.711 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 16.171 r_dihedral_angle_3_deg 14.183 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.631 r_scbond_it 2.262 r_angle_refined_deg 1.464 r_mcangle_it 1.259 r_mcbond_it 0.711 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12854 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction