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_angle_refined_deg 1.649
r_dihedral_angle_2_deg 34.562
r_mcbond_it 0.703
r_dihedral_angle_4_deg 20.646
r_dihedral_angle_3_deg 21.173
r_scbond_it 1.803
r_chiral_restr 0.1
r_dihedral_angle_1_deg 6.231
r_mcangle_it 1.345
r_scangle_it 3.16
r_bond_refined_d 0.016
r_gen_planes_refined 0.007
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

Software
Software Name Purpose
DNA data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
MOSFLM data reduction
SCALA data scaling