X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 168.68 α = 90
b = 223.52 β = 100.54
c = 193.94 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
-- -- -- 2006-03-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- 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
3.4 50 98.3 -- 0.144 -- 5.3 -- 94186 -- -3.0 --
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)
3.4 3.52 90.8 -- 0.562 2.0 4.3 --

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 3.41 50.0 -- -- -- 89433 4732 97.97 -- 0.26883 0.26635 0.31632 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 3.409 3.498 -- 303 5822 0.386 0.392 -- 86.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 116.893
Anisotropic B[1][1] 4.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -7.2
Anisotropic B[2][2] -3.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.81
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.429
r_dihedral_angle_3_deg 19.852
r_nbd_refined 0.259
r_angle_refined_deg 1.594
r_dihedral_angle_2_deg 36.909
r_chiral_restr 0.102
r_nbtor_refined 0.316
r_dihedral_angle_1_deg 8.144
r_mcbond_it 1.898
r_symmetry_hbond_refined 0.334
r_scangle_it 2.533
r_symmetry_vdw_refined 0.276
r_xyhbond_nbd_refined 0.184
r_gen_planes_refined 0.005
r_mcangle_it 2.332
r_bond_refined_d 0.015
r_dihedral_angle_4_deg 14.699
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28587
Nucleic Acid Atoms 1064
Heterogen Atoms 71
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019