X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 293.0
Details NaCl, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.89 α = 90
b = 101.89 β = 90
c = 122.01 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Yale mirrors 1999-03-01
Diffraction Radiation
Monochromator Protocol
yale mirrors, Ni/filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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 39.1 99.5 0.084 0.084 -- -- 49161 292821 0.0 0.0 17.0
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 2.03 99.8 0.49 -- 3.0 -- --

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 40.0 0.0 0.0 49962 49123 3917 98.3 0.199 0.199 0.195 0.214 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 2.06 3511 281 3230 0.236 0.244 0.015 85.6
X Ray Diffraction 2.06 2.13 4144 318 3826 0.217 0.249 0.014 99.7
X Ray Diffraction 2.13 2.2 4080 320 3760 0.207 0.226 0.013 99.8
X Ray Diffraction 2.2 2.29 4111 311 3800 0.203 0.22 0.012 99.8
X Ray Diffraction 2.29 2.39 4135 315 3820 0.208 0.233 0.013 99.7
X Ray Diffraction 2.39 2.52 4139 350 3789 0.205 0.231 0.012 100.0
X Ray Diffraction 2.52 2.68 4134 349 3785 0.204 0.224 0.012 99.7
X Ray Diffraction 2.68 2.88 4140 329 3811 0.199 0.228 0.013 100.0
X Ray Diffraction 2.88 3.17 4185 323 3862 0.201 0.22 0.012 99.9
X Ray Diffraction 3.17 3.63 4177 361 3816 0.178 0.198 0.01 99.9
X Ray Diffraction 3.63 4.58 4178 313 3865 0.164 0.186 0.011 98.9
X Ray Diffraction 4.58 39.1 4189 347 3842 0.205 0.208 0.011 95.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 24.68
Anisotropic B[1][1] 1.69
Anisotropic B[1][2] 1.82
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.39
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 0.59
x_torsion_deg 25.4
c_angle_d 1.2
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3471
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 386

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.1 refinement