X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details VAPOUR DIFFUSION HANGING DROP PROTEIN SOLUTION: 10 MG/ML IN 50 MM TRIS-HCL PH 7.0, 1 MM DTT, 20 MICROMOLAR PMSF RESERVOIR: 0.1 M SODIUM ACETATE,0.2 M AMMONIUM SULPHATE, 28% (V/V) PEG 4K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.95 α = 90
b = 130.41 β = 114.16
c = 81.32 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD MIRRORS 2001-09-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.97900,0.97937,0.88560 ESRF BM14

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 30 99.7 0.043 -- -- 3.4 -- 95532 -- -- --
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 2.03 97.0 0.157 -- 7.1 3.4 --

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 2.0 25.0 -- -- -- 95532 5022 99.6 -- 0.149 0.147 0.19 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 2.0 2.05 -- 319 6225 0.163 0.209 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.57
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.86
Anisotropic B[2][2] -0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.38
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_scbond_it 2.464
r_dihedral_angle_1_deg 6.011
r_gen_planes_refined 0.007
r_scangle_it 3.881
r_chiral_restr 0.108
r_nbtor_other 0.087
r_metal_ion_refined 0.064
r_symmetry_vdw_refined 0.256
r_xyhbond_nbd_refined 0.171
r_nbd_refined 0.227
r_mcbond_it 0.858
r_angle_other_deg 1.082
r_symmetry_vdw_other 0.296
r_angle_refined_deg 1.63
r_mcangle_it 1.536
r_bond_refined_d 0.017
r_nbd_other 0.255
r_gen_planes_other 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11443
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 1009

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing