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Crystal structure of RbcX point mutant Y17A/Y20L
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 1.5-2.5 M Sodium acetate, 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.94 75.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.446 α = 90 b = 93.446 β = 90 c = 411.544 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 2006-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.00000 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 3.4 103.142 99.6 0.089 0.089 3.4 3.4 26126
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 3.4 3.58 99.8 0.503 0.503 1.5 3.6 3742
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 3.4 20 25915 1319 99.28 0.255 0.253 0.2448 0.294 0.2904 RANDOM 106.428
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] -1.79 -1.79 3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.851 r_dihedral_angle_3_deg 23.28 r_dihedral_angle_4_deg 21.608 r_dihedral_angle_1_deg 5.837 r_scangle_it 2.404 r_angle_refined_deg 1.319 r_scbond_it 1.295 r_mcangle_it 1.012 r_mcbond_it 0.54 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.851 r_dihedral_angle_3_deg 23.28 r_dihedral_angle_4_deg 21.608 r_dihedral_angle_1_deg 5.837 r_scangle_it 2.404 r_angle_refined_deg 1.319 r_scbond_it 1.295 r_mcangle_it 1.012 r_mcbond_it 0.54 r_nbtor_refined 0.307 r_nbd_refined 0.256 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4727 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction MOLREP phasing