X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 292.0
Details 0.1 M Tris, o.5% v/v Jeffamine ED-2001, 3.5 M NaBr, pH 8.5, VAPOR DIFFUSION, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 170.65 α = 90
b = 170.65 β = 90
c = 46.83 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Single Silicon (111) monochromator 2011-02-14
Diffraction Radiation
Monochromator Protocol
Single crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.87 ESRF ID23-1

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
2.8 46.3 93.7 0.19 -- -- 4.6 16386 15483 3.0 3.0 36.0
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)
2.8 2.87 95.9 0.69 -- 2.6 5.0 2243

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 2.8 46.3 3.0 3.0 16386 15483 833 92.29 -- 0.22512 0.22262 0.27022 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 2.8 2.873 -- 76 1143 0.301 0.421 -- 95.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.889
Anisotropic B[1][1] 0.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.05
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.16
r_scbond_it 1.803
r_mcangle_it 1.345
r_mcbond_it 0.703
r_gen_planes_refined 0.007
r_chiral_restr 0.1
r_dihedral_angle_4_deg 20.646
r_dihedral_angle_3_deg 21.173
r_dihedral_angle_2_deg 34.562
r_dihedral_angle_1_deg 6.231
r_angle_refined_deg 1.649
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3779
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 37

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
MOLREP model building
DNA data collection