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Crystal structure of Oryza sativa DWARF14 (D14)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WOM PDB ENTRY 1WOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 8% PEG6000, 5% MPD, 0.1M Na-HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.988 α = 90 b = 88.191 β = 90 c = 121.231 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 RAYONIX MX225HE mirros 2010-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 1.45 50 100 0.053 5.3 91864 91864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 100 0.617 3.3 6.4 9084
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 1WOM 1.45 25.62 86870 4583 99.7 0.16209 0.16041 0.1606 0.19378 0.1948 RANDOM 13.313
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] -0.02 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.186 r_dihedral_angle_4_deg 18.593 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 5.806 r_scangle_it 5.264 r_scbond_it 3.522 r_angle_refined_deg 2.54 r_mcangle_it 2.455 r_mcbond_it 1.466 r_chiral_restr 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.186 r_dihedral_angle_4_deg 18.593 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 5.806 r_scangle_it 5.264 r_scbond_it 3.522 r_angle_refined_deg 2.54 r_mcangle_it 2.455 r_mcbond_it 1.466 r_chiral_restr 0.176 r_bond_refined_d 0.029 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4073 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 59
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling