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Crystal structure of CutA1 from Oryza sativa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZFH PDB ENTRY 2ZFH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 1.8M Ammonium sulfate, 0.09M tri-Sodium citrate dihydrate pH5.6, 0.18M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.214 α = 90 b = 127.214 β = 90 c = 121.868 γ = 90
Symmetry Space Group I 41 2 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 RIGAKU JUPITER 210 mirrors 2006-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
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 3.02 63.628 100 0.061 0.061 8 10.3 10138 10138 76.463
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 3.02 3.1 100 0.231 0.231 3.1 10.9 742
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 (All) 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 2ZFH 3.02 63.61 9635 490 100 0.18237 0.18237 0.17826 0.19 0.26674 0.2711 RANDOM 55.314
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] 0.78 0.78 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.699 r_dihedral_angle_3_deg 20.566 r_dihedral_angle_4_deg 17.239 r_dihedral_angle_1_deg 9.728 r_scangle_it 2.874 r_angle_refined_deg 2.204 r_scbond_it 1.956 r_mcangle_it 1.38 r_mcbond_it 1.097 r_angle_other_deg 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.699 r_dihedral_angle_3_deg 20.566 r_dihedral_angle_4_deg 17.239 r_dihedral_angle_1_deg 9.728 r_scangle_it 2.874 r_angle_refined_deg 2.204 r_scbond_it 1.956 r_mcangle_it 1.38 r_mcbond_it 1.097 r_angle_other_deg 1.023 r_symmetry_vdw_other 0.284 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.201 r_nbd_other 0.191 r_nbtor_refined 0.189 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.173 r_mcbond_other 0.162 r_chiral_restr 0.123 r_nbtor_other 0.099 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing