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Crystal structure of the Esterase domain from Rhodothermus marinus Rmar_1206 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FUK 2FUK, 3TRD, 3PF9 experimental model PDB 3TRD 2FUK, 3TRD, 3PF9 experimental model PDB 3PF9 2FUK, 3TRD, 3PF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 Protein at 15 mg/ml was crystallized by sitting drop vapour diffusion with 100 nl drops of protein supplemented with 100 nl of mother liquor comprising 0.2 M ammonium citrate dibasic, pH 5.0, 20 % w/v PEG 3350 (Hampton PEG/Ion HT96 screen D12), drops were equilibrated against 70 ul of mother liquor for one month before crystals appeared.
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.325 α = 90 b = 74.069 β = 113.47 c = 60.953 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 PIXEL DECTRIS PILATUS 2M 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.56 44.62 99.09 0.044 13.91 3.7 255878 69888
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 1.56 1.612 98.48 0.725 1.88 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2FUK, 3TRD, 3PF9 1.56 44.62 1.35 69880 3544 99.08 0.1458 0.1442 0.1462 0.1762 0.178 Random Selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.245 f_angle_d 1.179 f_chiral_restr 0.047 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3584 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing