X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 30% PEG1500, 0.1M MIB buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.93 α = 90
b = 62.38 β = 90
c = 62.87 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-07-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 1.072 ESRF BM14

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
1.25 44.28 89.1 0.047 -- -- 7.8 -- 46971 -- -- 9.7
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)
1.25 1.32 53.4 0.181 -- 7.5 5.8 4015

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 1.25 44.28 -- -- -- 44554 2377 88.78 -- 0.12073 0.119 0.15315 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 1.25 1.282 -- 97 1683 0.126 0.181 -- 46.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.897
Anisotropic B[1][1] -0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 8.076
r_sphericity_free 23.511
r_rigid_bond_restr 6.267
r_gen_planes_other 0.001
r_gen_planes_refined 0.01
r_chiral_restr 0.131
r_dihedral_angle_4_deg 11.859
r_dihedral_angle_3_deg 11.273
r_dihedral_angle_2_deg 27.001
r_dihedral_angle_1_deg 5.429
r_angle_other_deg 1.091
r_angle_refined_deg 1.842
r_bond_other_d 0.002
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1555
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 373

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
MOLREP model building
DNA data collection