X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 295.0
Details PEG 4000, tris hydrochloric acid, sodium acetate, guanosine diphosphate, 5'-adenyly-diphosphate-monothiophosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.07 α = 90
b = 110.07 β = 90
c = 171 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 MIRRORS 2004-08-29
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
SI(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 0.9794 ALS 8.2.1
SYNCHROTRON ALS BEAMLINE 8.2.1 0.9184, 0.9793 ALS 8.2.1

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
2.7 50 0.154 0.066 0.066 -- 5.8 -- 21160 2.0 2.0 55.835
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)
2.7 2.8 98.5 0.346 0.346 2.84 5.2 4101

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
MAD 2.7 20.0 2.0 2.0 -- 20020 1091 100.0 -- 0.22439 0.22162 0.27617 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 2.7 2.769 -- 59 1432 0.274 0.384 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.103
Anisotropic B[1][1] 1.29
Anisotropic B[1][2] 0.64
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.93
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.981
r_dihedral_angle_1_deg 5.285
r_mcangle_it 0.463
r_symmetry_hbond_refined 0.128
r_scbond_it 0.579
r_dihedral_angle_4_deg 15.336
r_nbd_refined 0.194
r_dihedral_angle_3_deg 17.281
r_bond_refined_d 0.005
r_metal_ion_refined 0.158
r_gen_planes_refined 0.003
r_angle_refined_deg 1.059
r_dihedral_angle_2_deg 36.056
r_symmetry_vdw_refined 0.177
r_chiral_restr 0.071
r_nbtor_refined 0.3
r_mcbond_it 0.245
r_xyhbond_nbd_refined 0.146
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4688
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 87

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data reduction
SCALEPACK data scaling
SOLVE phasing