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Crystal structure of a ribose 5-phosphate isomerase rpib (tm1080) from thermotoga maritima at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 40 % (+/-)-2-Methyl-2,4-Pentanediol; 0.1 M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.56 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.49 α = 90 b = 73.89 β = 90 c = 87.74 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 4 FLAT MIRROR,SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR 2002-11-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.91837, 0.97931, 0.97892 SSRL BL9-1
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 1.9 29.788 99.1 0.067 15 4.7 15973
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 1.9 1.95 93.2 0.284 3.4 2.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.9 28.26 15168 803 100 0.118 0.117 0.1199 0.138 0.1442 random 13.98
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] 1.4 -1.1 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.571 r_dihedral_angle_4_deg 15.732 r_dihedral_angle_3_deg 11.572 r_dihedral_angle_1_deg 5.529 r_scangle_it 4.246 r_scbond_it 2.562 r_angle_refined_deg 1.518 r_mcangle_it 1.467 r_angle_other_deg 0.934 r_mcbond_it 0.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.571 r_dihedral_angle_4_deg 15.732 r_dihedral_angle_3_deg 11.572 r_dihedral_angle_1_deg 5.529 r_scangle_it 4.246 r_scbond_it 2.562 r_angle_refined_deg 1.518 r_mcangle_it 1.467 r_angle_other_deg 0.934 r_mcbond_it 0.772 r_symmetry_vdw_other 0.308 r_symmetry_hbond_refined 0.259 r_xyhbond_nbd_refined 0.24 r_nbd_other 0.239 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.178 r_chiral_restr 0.1 r_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1139 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement SCALA data scaling RESOLVE model building SOLVE phasing CNS refinement MOSFLM data reduction XFIT data reduction CCP4 data scaling RESOLVE phasing