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Structural insights into substrate and cofactor selection 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 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.957 α = 90 b = 117.181 β = 90 c = 181.98 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 CCD ADSC QUANTUM 315r 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.69 50 92.1 0.043 12.2 89961 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 1.7 1.73 75.9
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 3JZ4 1.69 42.41 89961 4735 91.81 0.16751 0.16564 0.1712 0.20342 0.2081 RANDOM 13.46
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] 0.19 -0.18 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.433 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 12.533 r_dihedral_angle_1_deg 5.632 r_scangle_it 3.244 r_scbond_it 2.033 r_angle_refined_deg 1.257 r_mcangle_it 1.035 r_mcbond_it 0.679 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.433 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 12.533 r_dihedral_angle_1_deg 5.632 r_scangle_it 3.244 r_scbond_it 2.033 r_angle_refined_deg 1.257 r_mcangle_it 1.035 r_mcbond_it 0.679 r_nbtor_refined 0.307 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6890 Nucleic Acid Atoms Solvent Atoms 1149 Heterogen Atoms 110
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling