X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.58 α = 90
b = 70.93 β = 99.4
c = 82.01 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-06-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 0.97 SLS X06DA

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
2.07 53.38 99.8 0.123 0.122 -- 4.4 148474 33607 -- 4.0 --
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)
2.07 2.18 100.0 0.499 -- 4.0 -- --

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 2.07 53.38 -- -- 33657 31727 1693 99.34 -- 0.19022 0.18705 0.24987 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 2.07 2.124 -- 134 2342 0.23 0.324 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.386
Anisotropic B[1][1] 0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.26
Anisotropic B[2][2] 1.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.663
r_scbond_it 3.087
r_mcangle_it 1.861
r_mcbond_it 1.113
r_gen_planes_refined 0.01
r_chiral_restr 0.127
r_dihedral_angle_4_deg 18.096
r_dihedral_angle_3_deg 16.724
r_dihedral_angle_2_deg 38.74
r_dihedral_angle_1_deg 6.787
r_angle_refined_deg 1.996
r_bond_refined_d 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4174
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 430

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0102 refinement
AMoRE model building
DNA data collection