X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Dialysis
pH 7.5
Temperature 277.15
Details CRYSTALS GROWN AT 277 K IN 0.010 M TRIS-HCL PH 7.5, 0.012 M MGCL2, 0.002 M SPERMINE, 6% 1,6-HEXANEDIOL. CRYOPROTECTION CONDITIONS: AFTER WASHING IN FRESH CRYSTALLIZATION SOLUTION FOR 10 MIN AND ADDITION OF 30% MPD (V/V), CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN, DIALYSIS, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.25 α = 90
b = 32.99 β = 90.38
c = 61.88 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 1999-04-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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 25.8 88.6 -- 0.036 -- 3.1 13678 13678 0.0 0.0 29.3
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 2.1 70.7 -- 0.171 2.2 2.6 --

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
-- 2.0 25.79 0.0 0.0 13678 13678 926 88.5 0.227 0.227 0.227 0.263 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 2.11 -- 101 1432 0.324 0.38 0.038 70.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 53.6
Anisotropic B[1][1] 1.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.76
Anisotropic B[2][2] -0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.3
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.3
c_bond_d 0.009
c_angle_deg 1.4
c_dihedral_angle_d 12.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.42
Luzzati Sigma A (R-Free Set) 0.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1652
Heterogen Atoms 24
Solvent Atoms 220

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK, SOLVE Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building