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GDP-BOUND YPT7P AT 1.35 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other YPT7-GPPNHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG, HEPES, GDP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.98 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.535 α = 90 b = 55.43 β = 90 c = 60.177 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 MARRESEARCH MIRROR 2000-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.35 25 98.6 0.081 15.77 5.4 36543 36543 14.7
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) 1.35 1.45 97.3 0.308 4.33 4.2 6841
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT YPT7-GPPNHP 1.35 22.61 36545 36545 2413 98.4 0.191 0.191 0.161 0.227 0.2369 RANDOM 20.1
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] -0.1 2.01 -1.92
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.083 s_non_zero_chiral_vol 0.069 s_similar_adp_cmpnt 0.062 s_zero_chiral_vol 0.053 s_angle_d 0.029 s_from_restr_planes 0.0282 s_anti_bump_dis_restr 0.014 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1271 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 29
Software Software Software Name Purpose AMoRE phasing SHELXL-97 refinement MAR345 data collection XDS data scaling