X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 163.87 α = 90
b = 36.97 β = 125.66
c = 99.99 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-01-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.00 SSRL BL7-1

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
1.9 50 98.8 0.075 -- -- 3.5 -- 38838 -- -1.0 --
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)
1.9 1.97 92.6 0.356 -- -- 3.2 3626

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
FOURIER SYNTHESIS 1.9 40.62 -- 0.0 40660 37002 3658 94.86 -- 0.1954 0.1911 0.2356 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 1.9 1.949 -- 240 2089 0.237 0.288 -- 81.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.3794
Anisotropic B[1][1] -1.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.05
Anisotropic B[2][2] -0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.358
r_nbd_refined 0.191
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.11
r_dihedral_angle_4_deg 17.072
r_dihedral_angle_3_deg 13.847
r_dihedral_angle_2_deg 32.863
r_dihedral_angle_1_deg 5.98
r_angle_other_deg 1.071
r_angle_refined_deg 1.31
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_nbd_other 0.193
r_nbtor_refined 0.182
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.139
r_xyhbond_nbd_other 0.013
r_symmetry_vdw_refined 0.106
r_symmetry_vdw_other 0.209
r_symmetry_hbond_refined 0.11
r_mcbond_it 0.724
r_mcbond_other 0.121
r_mcangle_it 0.813
r_scbond_it 1.673
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2686
Nucleic Acid Atoms 262
Heterogen Atoms 99
Solvent Atoms 227

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.2.0019 refinement
SCALEPACK data reduction
DENZO data collection