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Crystal structure of RbcX in complex with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PEN PDB entry 2PEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.4 M Sodium acetate, 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.83 74.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.207 α = 90 b = 93.207 β = 90 c = 412.016 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 CCD ADSC QUANTUM 315 2006-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97600 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.95 103.142 96.6 0.08 0.08 5.7 3.7 37874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.11 97.6 0.536 0.536 1.4 3.8 5500
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 PDB entry 2PEN 2.95 20 37701 1913 95.62 0.236 0.235 0.2294 0.264 0.2603 RANDOM 68.682
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] -0.25 -0.25 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_3_deg 22.154 r_dihedral_angle_4_deg 20.682 r_dihedral_angle_1_deg 5.394 r_scangle_it 2.817 r_scbond_it 1.596 r_angle_refined_deg 1.388 r_mcangle_it 1.272 r_mcbond_it 0.688 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_3_deg 22.154 r_dihedral_angle_4_deg 20.682 r_dihedral_angle_1_deg 5.394 r_scangle_it 2.817 r_scbond_it 1.596 r_angle_refined_deg 1.388 r_mcangle_it 1.272 r_mcbond_it 0.688 r_nbtor_refined 0.314 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5216 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction MOLREP phasing