X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
Temperature 293.0
Details 24% NP_PEG 4000, 0.065M Tris_base, 0.16M Mg Cl, 0.035M Tris Cl, 20% Glycerol, CuCl2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Method Vapor Diffusion Sitting Drop Nanodrop
Temperature 293.0
Details 24% NP_PEG 4000, 0.065M Tris_base, 0.16M Mg Cl, 0.035M Tris Cl, 20% Glycerol, CuCl2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.3 α = 90
b = 104.66 β = 90
c = 286.61 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2003-09-22
CCD ADSC -- 2003-09-11
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) SINGLE WAVELENGTH
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 0.979686, 0.979835, 1.020026 ALS 8.3.1
SYNCHROTRON ALS BEAMLINE 8.2.1 -- ALS 8.2.1

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
2.5 28.66 98.6 0.067 -- -- 4.6 -- 49807 -- -- 82.46
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)
2.5 2.64 93.3 0.727 -- 2.3 3.0 6756

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 2.6 28.66 -- -- -- 42483 2243 99.3 -- 0.22399 0.22144 0.27227 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 2.6 2.668 -- 164 2935 0.37 0.398 -- 94.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.826
Anisotropic B[1][1] 6.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.51
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.77
r_dihedral_angle_3_deg 19.325
r_dihedral_angle_1_deg 7.582
r_angle_refined_deg 1.595
r_dihedral_angle_2_deg 37.594
r_nbd_refined 0.248
r_dihedral_angle_4_deg 20.523
r_gen_planes_refined 0.006
r_angle_other_deg 0.873
r_nbd_other 0.184
r_xyhbond_nbd_refined 0.145
r_mcangle_it 2.341
r_scbond_it 4.206
r_bond_refined_d 0.016
r_nbtor_refined 0.199
r_mcbond_it 1.535
r_symmetry_vdw_refined 0.129
r_mcbond_other 0.492
r_bond_other_d 0.003
r_xyhbond_nbd_other 0.019
r_gen_planes_other 0.001
r_nbtor_other 0.092
r_symmetry_vdw_other 0.202
r_chiral_restr 0.085
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9010
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 22

Software

Software
Software Name Purpose
XDS data scaling
SCALA data scaling
SHELXD phasing version: + AutoSHARP
REFMAC refinement version: 5.2.0005
XDS data reduction
CCP4 data scaling version: (SCALA)
autoSHARP phasing