X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 298.0
Details 2.5 M NaCl, 10% MPD, 0.1M CAPS pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.31 α = 90
b = 108.45 β = 90
c = 141.3 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2007-02-27
CCD ADSC QUANTUM 315 -- 2007-02-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
SYNCHROTRON NSLS BEAMLINE X3A 0.9793 NSLS X3A

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
1.8 50 98.3 0.051 0.041 -- 9.1 40015 40015 0.0 0.0 --
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)
1.8 1.86 100.0 0.48 0.424 2.3 7.2 3999

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
SAD 1.8 43.19 0.0 0.0 39802 39802 2006 97.57 0.208 0.208 0.207 0.23 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 1.8 1.842 2839 144 2695 0.277 0.315 -- 96.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.133
Anisotropic B[1][1] 0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 18.461
r_chiral_restr 0.086
r_dihedral_angle_3_deg 13.823
r_nbd_refined 0.208
r_nbtor_refined 0.298
r_scangle_it 3.914
r_scbond_it 2.301
r_symmetry_vdw_refined 0.343
r_mcbond_it 0.814
r_angle_refined_deg 1.202
r_dihedral_angle_1_deg 4.834
r_dihedral_angle_2_deg 34.638
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.143
r_mcangle_it 1.523
r_bond_refined_d 0.011
r_symmetry_hbond_refined 0.179
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2368
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 212

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
HKL-2000 data reduction
SHELXE model building
SHELXD phasing