X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
Temperature 277.0
Details 18% PEG MME 2000, 0.04M Tris_base, 0.06M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.58 α = 90
b = 70.58 β = 90
c = 205.36 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 ADSC Flat mirror 2004-05-20
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator SINGLE WAVELENGTH
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1
SYNCHROTRON SSRL BEAMLINE BL9-1 0.879288, 0.978780, 0.979359 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
2.38 29.29 99.9 -- 0.076 -- 6.9 -- 24673 -- -- 61.62
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)
2.38 2.51 99.6 -- 0.7 2.3 5.9 3515

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 2.38 29.29 -- -- -- 23362 1256 99.82 -- 0.19271 0.19035 0.23799 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 2.38 2.442 -- 92 1713 0.294 0.346 -- 99.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.978
Anisotropic B[1][1] -3.57
Anisotropic B[1][2] -1.78
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.35
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.208
r_symmetry_vdw_refined 0.119
r_dihedral_angle_4_deg 15.146
r_xyhbond_nbd_refined 0.129
r_symmetry_hbond_refined 0.172
r_scbond_it 6.435
r_bond_refined_d 0.017
r_mcbond_it 2.225
r_chiral_restr 0.114
r_mcangle_it 3.719
r_dihedral_angle_1_deg 6.475
r_dihedral_angle_3_deg 16.513
r_dihedral_angle_2_deg 40.701
r_gen_planes_refined 0.005
r_angle_refined_deg 1.508
r_scangle_it 8.737
r_nbtor_refined 0.308
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2739
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 83

Software

Software
Software Name Purpose
XDSauto data collection
SCALA data scaling version: 4.2)
SHARP phasing
autoSHARP phasing
SOLOMON phasing
REFMAC refinement version: 5.2.0005
XDS data reduction
CCP4 data scaling version: (SCALA)