X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 289.0
Details 0.04M Sodium dihydrogen phosphate, 0.96M Di-potassium hydrogen phosphate, GTP, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.52 α = 119.25
b = 71.58 β = 110.18
c = 71.51 γ = 99.58
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-3 Mirrors 2007-10-29
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
1.53 50 94.1 -- 0.069 -- 4.5 149957 149957 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.53 1.58 76.5 -- 0.359 2.4 3.9 12259

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 1.53 26.16 -- 0.0 142270 142270 7527 93.89 0.145 0.145 0.143 0.183 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.53 1.57 1198 396 7702 0.178 0.258 -- 68.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.199
Anisotropic B[1][1] -0.62
Anisotropic B[1][2] -0.18
Anisotropic B[1][3] -0.29
Anisotropic B[2][2] 0.89
Anisotropic B[2][3] 1.12
Anisotropic B[3][3] 0.57
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.446
r_sphericity_free 6.274
r_rigid_bond_restr 1.995
r_scangle_it 4.393
r_scbond_it 3.208
r_mcangle_it 2.289
r_mcbond_it 1.52
r_nbd_refined 0.233
r_gen_planes_refined 0.007
r_chiral_restr 0.112
r_dihedral_angle_4_deg 11.071
r_dihedral_angle_3_deg 13.391
r_dihedral_angle_2_deg 40.448
r_dihedral_angle_1_deg 6.13
r_angle_refined_deg 1.578
r_bond_refined_d 0.015
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.178
r_metal_ion_refined 0.124
r_symmetry_vdw_refined 0.226
r_symmetry_hbond_refined 0.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8197
Nucleic Acid Atoms 0
Heterogen Atoms 94
Solvent Atoms 1177

Software

Computing
Computing Package Purpose
SBC-COLLECT, HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL-3000, SHELX, MLPHARE, RESOLVE, ARP/wARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement