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Mutant nitrobindin M75L/H76L/Q96C/M148L (NB4H) from Arabidopsis thaliana with cofactor MnPPIX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.6 285.15 1:1 mixture (2 uL total volume) of protein (20 mg/mL) and precipitant solution containing 100 mM Tris/HCl pH 8.6, 18 % (w/v) PEG 2000; 30% (v/v) Ethylene glycol were added as cryo-protectant before harvesting and flash freezing in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.9 α = 90 b = 79.547 β = 90 c = 36.56 γ = 90
Symmetry Space Group P 21 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 6M 2020-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976253 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.1375 39.774 99.94 0.075 0.078 0.022 0.998 14.5 12.2 64928 14.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1375 1.157 100 1.037 1.088 0.325 0.8107 2.164 10.93
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3WJB 1.14 39.77 1.33 64903 3158 99.86 0.1451 0.1445 0.1452 0.1581 0.1592 21.64
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 12.3489 f_angle_d 1.3395 f_chiral_restr 0.1204 f_plane_restr 0.0157 f_bond_d 0.0122
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1198 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement Coot model building BUCCANEER model building PHASER phasing Aimless data scaling XDS data reduction MxCuBE data collection