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Structural insights into substrate and cofactor selelction by sp2771
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 PEG 5000 MME, Tascimate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.986 α = 90 b = 115.626 β = 90 c = 180.533 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 IMAGE PLATE RIGAKU RAXIS IV 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 95.9 0.062 4.9 48792 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 96.2
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 THROUGHOUT 3JZ4 2.1 50 2 48792 2594 95.84 0.17461 0.17186 0.1749 0.22586 0.2299 RANDOM 20.755
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] 0.01 -0.36 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_4_deg 19.674 r_dihedral_angle_3_deg 14.985 r_dihedral_angle_1_deg 6.352 r_scangle_it 3.429 r_scbond_it 2.145 r_angle_refined_deg 1.385 r_mcangle_it 1.124 r_mcbond_it 0.699 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_4_deg 19.674 r_dihedral_angle_3_deg 14.985 r_dihedral_angle_1_deg 6.352 r_scangle_it 3.429 r_scbond_it 2.145 r_angle_refined_deg 1.385 r_mcangle_it 1.124 r_mcbond_it 0.699 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6882 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling