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Crystal structure of GNIP1Aa from Chromobacterium piscinae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 100 mM citrate, pH 5.6, 2 % Tacsimate, pH 5.0, 14 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.676 α = 90 b = 143.187 β = 90 c = 209.62 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 OXFORD ONYX CCD 2010-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.5 15 96.6 0.111 0.129 11.9 3.72 79981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 97.7 0.364 0.429 3.58
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SIRAS FREE R-VALUE 2.5 14.988 79981 4016 96.675 0.233 0.2304 0.2332 0.2714 0.2735 27.052
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] 1.331 -0.545 -0.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.406 r_dihedral_angle_4_deg 17.21 r_dihedral_angle_3_deg 15.92 r_dihedral_angle_1_deg 6.679 r_lrange_it 5.59 r_lrange_other 5.583 r_scangle_it 3.549 r_scangle_other 3.549 r_mcangle_it 3.389 r_mcangle_other 3.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.406 r_dihedral_angle_4_deg 17.21 r_dihedral_angle_3_deg 15.92 r_dihedral_angle_1_deg 6.679 r_lrange_it 5.59 r_lrange_other 5.583 r_scangle_it 3.549 r_scangle_other 3.549 r_mcangle_it 3.389 r_mcangle_other 3.389 r_scbond_it 2.117 r_scbond_other 2.116 r_mcbond_it 2.03 r_mcbond_other 2.029 r_angle_refined_deg 1.55 r_angle_other_deg 0.961 r_symmetry_nbd_refined 0.231 r_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_refined 0.19 r_nbtor_refined 0.171 r_symmetry_nbd_other 0.156 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_6 0.057 r_ncsr_local_group_5 0.056 r_ncsr_local_group_3 0.052 r_ncsr_local_group_2 0.044 r_ncsr_local_group_4 0.043 r_ncsr_local_group_1 0.041 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16136 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CRANK phasing