X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 30% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.73 α = 90
b = 63.42 β = 91.27
c = 67.94 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-10-21
CCD MARRESEARCH -- 2001-08-03
Diffraction Radiation
Monochromator Protocol
Si 111 MAD
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9A 0.98167, 0.98147 NSLS X9A
SYNCHROTRON NSLS BEAMLINE X9A 0.97962 NSLS X9A

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
2.05 20 97.5 0.031 -- -- -- 19149 19149 0.0 0.0 10.2
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)
2.03 2.13 99.9 0.049 -- -- -- --

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 2.05 19.58 -- 0.0 18666 18666 1874 97.5 0.2216 0.217 0.217 0.271 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 2.05 2.18 -- 342 2823 0.195 0.279 0.015 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.9
Anisotropic B[1][1] 2.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.58
Anisotropic B[2][2] 1.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.82
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 7.08
c_scbond_it 5.42
c_mcangle_it 4.37
c_mcbond_it 3.59
c_improper_angle_d 0.93
c_dihedral_angle_d 20.5
c_angle_deg 1.7
c_bond_d 0.011
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) -0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2414
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 258

Software

Computing
Computing Package Purpose
MARMAD, DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE, MLPHARE, DM Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SnB/MLPHARE/DM model building