X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 170.53 α = 90
b = 222.28 β = 102.19
c = 194.81 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 MARMOSAIC 325 mm CCD -- 2007-06-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1

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
3.38 50 92.3 -- -- -- 2.5 -- 90557 -- -- --
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)
3.38 3.5 89.2 -- -- 1.5 2.2 --

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
MOLECULAR REPLACEMENT 3.38 50.0 -- -- -- 85851 4515 91.06 -- 0.27285 0.27028 0.32168 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 3.38 3.47 -- 293 5108 0.43 0.45 -- 74.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 96.182
Anisotropic B[1][1] 1.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -11.68
Anisotropic B[2][2] -4.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.11
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.882
r_mcbond_it 0.656
r_dihedral_angle_3_deg 24.019
r_bond_refined_d 0.013
r_scbond_it 1.071
r_dihedral_angle_1_deg 7.947
r_nbtor_refined 0.319
r_mcangle_it 1.168
r_symmetry_vdw_refined 0.295
r_chiral_restr 0.11
r_angle_refined_deg 1.613
r_dihedral_angle_4_deg 18.674
r_nbd_refined 0.273
r_dihedral_angle_2_deg 39.538
r_symmetry_hbond_refined 0.284
r_xyhbond_nbd_refined 0.211
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28140
Nucleic Acid Atoms 1107
Heterogen Atoms 9
Solvent Atoms 0

Software

Software
Software Name Purpose
MAR345 data collection version: CCD
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
SCALEPACK data scaling