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X-ray structure of gene product from arabidopsis thaliana at1g77540
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 PROTEIN 10 MG/ML, 29% MEPEG 5K,
0.100 M SODIUM CITRATE, 0.100 M PIPES, CRYOPROTRECTED CRYSTAL
SOAKED IN 1 M SODIUM BROMIDE FOR CIRCA 40 SECONDS, pH 6.5, Vapor diffusion, hanging drop, temperature 277 KK
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.349 α = 90 b = 60.601 β = 91.5 c = 29.424 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm RH MIRROR 2004-08-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.926676, 0.926676, 0.919801, 0.919528, 0.91302 APS 32-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.15 20.29 95.9 0.039 16.5 3.5 32713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.15 1.18 70.7 0.345 2.22 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD (BROMIDE PHASING) THROUGHOUT 1.15 30.303 31030 1658 95.95 0.149 0.149 0.1476 0.1458 0.1703 0.1723 RANDOM 17.748
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] -0.306 0.031 0.039 0.269
RMS Deviations Key Refinement Restraint Deviation Sphericity. Free atoms 6.792 r_scangle_it 6.788 Sphericity. Bonded atoms 6.321 r_dihedral_angle_1_deg 5.835 r_scbond_it 4.668 r_mcangle_it 3.96 r_mcbond_it 2.75 Rigid bond restraints 2.382 r_angle_refined_deg 2.022 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation Sphericity. Free atoms 6.792 r_scangle_it 6.788 Sphericity. Bonded atoms 6.321 r_dihedral_angle_1_deg 5.835 r_scbond_it 4.668 r_mcangle_it 3.96 r_mcbond_it 2.75 Rigid bond restraints 2.382 r_angle_refined_deg 2.022 r_nbtor_refined 0.326 r_xyhbond_nbd_refined 0.262 r_symmetry_hbond_refined 0.256 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.227 r_chiral_restr 0.152 r_bond_refined_d 0.021 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 805 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS phasing CNS refinement REFMAC refinement PHENIX phasing ARP/wARP model building