X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 18.0
Details 0.05 M Cacodylate (pH 6.5), 0.05 M NaCl, 2.5% PEG 8K, 20% glycerol, 0.3 mM n-Nonyl-beta-D-thiomaltoside, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 18K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.25 α = 90
b = 204.65 β = 96.54
c = 147.79 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2003-01-19
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.00 ALS 8.3.1

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 50 95.7 0.04 0.05 -- -- 77507 64912 2.5 2.5 92.0
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)
3.0 3.12 95.0 0.274 0.332 2.5 2.2 --

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 3.0 20.0 -- 3.0 77507 70421 3727 95.7 -- 0.27381 0.27084 0.30369 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 3.0 3.124 -- 245 4648 0.418 0.523 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.251
Anisotropic B[1][1] 0.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.66
Anisotropic B[2][2] 1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.37
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.579
r_bond_refined_d 0.01
r_angle_refined_deg 1.252
r_dihedral_angle_1_deg 7.096
r_chiral_restr 0.107
r_gen_planes_refined 0.005
r_nbd_refined 0.248
r_xyhbond_nbd_refined 0.165
r_symmetry_vdw_refined 0.225
r_symmetry_hbond_refined 0.06
r_mcbond_it 0.575
r_mcangle_it 1.098
r_scbond_it 1.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18846
Nucleic Acid Atoms 200
Heterogen Atoms 186
Solvent Atoms 14

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement