X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.1
Temperature 293.0
Details PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.86 α = 90
b = 114.51 β = 96.17
c = 68.37 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 TOROIDAL FOCUSING MIRROR 2008-10-15
Diffraction Radiation
Monochromator Protocol
SI(111) CHANNEL CUT SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 0.979 NSLS X6A

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
1.9 50 95.8 0.117 -- -- 3.7 -- 87369 -- -- 28.7
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)
1.9 1.97 98.2 -- 0.698 1.7 3.6 8937

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
FOURIER SYNTHESIS 1.91 28.57 -- 0.0 -- 87311 4397 95.29 -- 0.198 0.196 0.236 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 1.91 1.956 -- 296 5781 0.379 0.399 -- 90.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.907
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.13
Anisotropic B[2][2] 0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.619
r_scbond_it 3.256
r_mcangle_it 3.547
r_mcbond_it 2.496
r_gen_planes_refined 0.004
r_chiral_restr 0.073
r_dihedral_angle_4_deg 17.166
r_dihedral_angle_3_deg 13.307
r_dihedral_angle_2_deg 34.702
r_dihedral_angle_1_deg 5.584
r_angle_refined_deg 1.084
r_bond_refined_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.145
Luzzati ESD (R-Free Set) 0.139
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6162
Nucleic Acid Atoms 0
Heterogen Atoms 311
Solvent Atoms 896

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
REFMAC 5.5.0070 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 version: 5.5.0070 refinement
HKL data processing