X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 293.0
Details Tris-HCl, Ammonium Sulfate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.5 α = 90
b = 57.5 β = 90
c = 79.5 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU -- 2002-03-04
Diffraction Radiation
Monochromator Protocol
MIRRORS + Si (111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.9000, 0.9785, 0.9791 SPring-8 BL45PX

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
1.94 31 96.8 0.083 -- -- 8.23 -- 11527 -- -3.0 23.6
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)
1.94 2.01 100.0 0.33 -- 3.4 8.39 1174

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
MAD 1.94 10.0 0.0 0.0 11035 11527 1078 95.0 -- -- 0.199 0.239 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 1.94 2.01 1080 110 970 0.239 0.253 -- 95.0
X Ray Diffraction 2.01 2.09 1129 124 -- 0.214 0.252 -- 97.0
X Ray Diffraction 2.09 2.18 1111 108 -- 0.219 0.232 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 30.7
Anisotropic B[1][1] -0.55
Anisotropic B[1][2] -1.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.1
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 2.52
c_angle_deg 1.564
c_scbond_it 3.5
c_scangle_it 4.95
c_improper_angle_d 0.791
c_dihedral_angle_d 26.117
c_mcbond_it 1.97
c_bond_d 0.013
Coordinate Error
Parameter Value
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.288
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1027
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 89

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
SHARP phasing
WARP model building
CNS refinement
ARP/wARP model building