X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.8
Temperature 298.0
Details 0.1M HEPES pH 7.8, 15% PEG 4K, 6% 2-Propanol, 40mM BME, and 3% Ethanol, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.01 α = 90
b = 43.21 β = 90
c = 158.22 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 130
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ varimax optics 2006-04-24
Diffraction Radiation
Monochromator Protocol
none SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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 50 94.3 0.056 -- -- 3.5 20427 19263 -1.0 -1.0 --
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)
2.0 2.07 78.8 0.193 -- 6.2 2.3 1587

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 2.0 50.0 0.0 0.0 19218 18215 973 94.78 0.23587 0.23587 0.23328 0.28678 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 2.0 2.052 1089 72 1089 0.283 0.309 -- 80.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.191
Anisotropic B[1][1] -0.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.25
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.189
r_nbtor_refined 0.301
r_symmetry_vdw_refined 0.105
r_chiral_restr 0.072
r_nbd_refined 0.176
r_mcbond_it 0.554
r_angle_refined_deg 1.105
r_mcangle_it 0.907
r_symmetry_hbond_refined 0.109
r_scbond_it 0.994
r_bond_refined_d 0.008
r_gen_planes_refined 0.003
r_scangle_it 1.444
r_xyhbond_nbd_refined 0.126
r_dihedral_angle_3_deg 13.747
r_dihedral_angle_2_deg 33.953
r_dihedral_angle_4_deg 14.852
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2189
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 140

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
CrystalClear data collection
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing