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Crystal structure of cce_0566 from the cyanobacterium Cyanothece 51142, a protein associated with nitrogen fixation from the DUF269 family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G7P pdb entry 3G7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, protein in 100 mM NaCl, 20 mM Tris, 1 mM DTT, pH 7.1. Protein 2 mg/mL, Mix 1.5 uL of protein and precipatant, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.079 α = 90 b = 44.573 β = 111.01 c = 67.724 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 ADSC QUANTUM 315 2008-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9792 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.59 33 91.692 38536 38536 19.938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.593 1.634 75.34 2312
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3G7P 1.59 33 38536 38536 2057 91.69 0.2123 0.21 0.2063 0.25452 0.2492 RANDOM 21.764
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] 1.08 0.72 -0.53 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.354 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 14.004 r_dihedral_angle_1_deg 6.349 r_scangle_it 5.562 r_scbond_it 3.548 r_mcangle_it 2.336 r_angle_refined_deg 2.19 r_mcbond_it 1.423 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.354 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 14.004 r_dihedral_angle_1_deg 6.349 r_scangle_it 5.562 r_scbond_it 3.548 r_mcangle_it 2.336 r_angle_refined_deg 2.19 r_mcbond_it 1.423 r_chiral_restr 0.143 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 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 2436 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling