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Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form MG atoms)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 298 PEG, pH 6.5, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.179 α = 90 b = 106.179 β = 90 c = 148.811 γ = 90
Symmetry Space Group P 41 21 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 MAR CCD 165 mm mirrors 2001-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.7 SPring-8 BL44B2
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 1.52 20 98.5 0.048 7.5 6.9 892176 128529
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) 1.52 1.57 94.6 0.252
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT free R 1.52 20 122094 6435 93.5 0.203 0.202 0.257 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 7489
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.073 s_non_zero_chiral_vol 0.047 s_zero_chiral_vol 0.037 s_from_restr_planes 0.0261 s_angle_d 0.024 s_anti_bump_dis_restr 0.019 s_bond_d 0.007 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6912 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building SHELXL-97 refinement X-PLOR phasing