X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.8
Temperature 25.0
Details 1.4M ammonium sulphate, cacodylate , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 25K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.5 α = 90
b = 118.42 β = 90
c = 70 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.978 SSRL BL9-1

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
2.3 70.7 93.5 -- 0.162 -- 3.1 26011 26011 0.0 0.0 37.1
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)
2.3 2.36 89.1 -- 0.423 1.65 2.7 1779

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 2.3 70.71 0.0 0.0 26011 24745 1266 93.4 0.207 0.207 0.205 0.24829 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 2.3 2.36 1779 99 1779 0.269 0.335 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 43.702
Anisotropic B[1][1] -2.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.4
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.854
r_scbond_it 1.176
r_mcangle_it 2.159
r_mcbond_it 1.277
r_symmetry_hbond_refined 0.196
r_symmetry_vdw_other 0.307
r_symmetry_vdw_refined 0.206
r_bond_refined_d 0.017
r_bond_other_d 0.001
r_angle_refined_deg 1.649
r_angle_other_deg 0.82
r_dihedral_angle_1_deg 6.296
r_chiral_restr 0.083
r_gen_planes_refined 0.007
r_gen_planes_other 0.004
r_nbd_refined 0.238
r_nbd_other 0.255
r_nbtor_other 0.092
r_xyhbond_nbd_refined 0.196
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.177
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4154
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 129

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement