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The crystal structure of Acinetobacter radioresistens CYP116B5 heme domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 100 mM amino acids (0.02 M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline), 0.1 M Gly-Gly, AMPD buffer pH 8.5, 50% v/v of 25% w/v PEG 4000, 40% w/v 1,2,6- Hexanetriol
Crystal Properties Matthews coefficient Solvent content 5.19 76.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.9 α = 90 b = 109.9 β = 90 c = 164.2 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS3 X 2M 2018-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 1.00 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.6 109.9 100 0.084 1 19.9 13.5 31654 73.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 100 0.584 1.5 12.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6GII 2.6 91.33 30052 100 0.2 0.2337 0.24 0.2618 RANDOM 88.6208
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3354 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement Coot model building DIALS data reduction Aimless data scaling PHASER phasing