X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 16% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.22 α = 78.58
b = 63.36 β = 89.08
c = 75.06 γ = 89.87
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2007-06-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.9998 SLS X10SA

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
2.38 73.57 98.0 0.069 0.069 -- 2.1 30547 29936 -- -- --
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)
2.38 2.51 96.9 0.126 0.126 4.6 1.9 4335

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
-- 2.38 73.52 -- 0.0 30558 29935 1518 97.96 -- 0.217 0.214 0.266 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 2.38 2.442 -- 94 2078 0.238 0.275 -- 96.15
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.348
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 0.08
Anisotropic B[1][3] -0.38
Anisotropic B[2][2] -0.38
Anisotropic B[2][3] 0.6
Anisotropic B[3][3] -0.34
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.717
r_scbond_it 2.415
r_mcangle_it 1.736
r_mcbond_it 1.006
r_symmetry_hbond_refined 0.255
r_bond_refined_d 0.018
r_angle_refined_deg 1.841
r_dihedral_angle_1_deg 8.24
r_dihedral_angle_2_deg 38.219
r_dihedral_angle_3_deg 17.903
r_dihedral_angle_4_deg 17.936
r_chiral_restr 0.127
r_gen_planes_refined 0.007
r_nbd_refined 0.224
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.206
r_symmetry_vdw_refined 0.214
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3925
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 168

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.000 data extraction
REFMAC5 refinement
SCALA data processing