X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 10
Temperature 298.0
Details 11 % PEG 8000, 0.1 M Gycine buffer pH 10.0, 0.001 M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.2 α = 90
b = 97.82 β = 90
c = 129.89 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD MIRRORS 2008-02-14
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B -- APS 23-ID-B

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 50 93.1 -- 0.114 -- 6.7 -- 62447 -- -3.0 --
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)
2.0 2.07 70.1 -- 0.637 1.585 4.8 --

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
SAD 2.008 44.5 -- -- 62371 59243 3127 92.92 -- 0.21295 0.21089 0.25248 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 2.008 2.06 -- 170 3111 0.353 0.4 -- 67.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.563
Anisotropic B[1][1] 1.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.71
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.131
r_mcangle_it 2.52
r_symmetry_hbond_refined 0.172
r_gen_planes_refined 0.005
r_scbond_it 3.472
r_dihedral_angle_4_deg 14.748
r_symmetry_vdw_refined 0.288
r_nbtor_refined 0.301
r_scangle_it 4.716
r_nbd_refined 0.201
r_dihedral_angle_1_deg 5.146
r_dihedral_angle_3_deg 15.116
r_chiral_restr 0.086
r_bond_refined_d 0.011
r_dihedral_angle_2_deg 39.896
r_angle_refined_deg 1.247
r_mcbond_it 1.82
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4579
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 315

Software

Software
Software Name Purpose
SOLVE phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling