X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details HANGING DROP: 5 MICROL PROTEIN + 5 MICROL RESEVOIR, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.5, 3 MM DTT, 150 MM NACL, 0.01% (V/V) C8E4 RESEVOIR: 22% (W/V) PEG10000, 100 MM HEPES PH 7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.04 α = 90
b = 114.04 β = 90
c = 76.46 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-04-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 -- BESSY 14.1

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
2.07 50 99.1 0.066 -- -- 9.4 -- 1440548 -- -- --
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)
2.07 2.11 96.8 0.182 -- 10.2 8.8 --

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
MAD 2.07 100.0 -- -- -- 32527 1735 99.0 -- 0.155 0.154 0.187 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 2.07 2.12 -- 133 2334 0.158 0.215 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.76
Anisotropic B[1][1] 0.75
Anisotropic B[1][2] 0.38
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.13
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.036
r_nbd_refined 0.304
r_symmetry_vdw_other 0.304
r_nbtor_other 0.101
r_scangle_it 3.913
r_scbond_it 2.638
r_angle_other_deg 1.019
r_symmetry_vdw_refined 0.088
r_xyhbond_nbd_refined 0.219
r_angle_refined_deg 2.109
r_mcbond_it 0.784
r_chiral_restr 0.11
r_gen_planes_refined 0.009
r_gen_planes_other 0.011
r_dihedral_angle_1_deg 6.404
r_nbd_other 0.255
r_mcangle_it 1.41
r_symmetry_hbond_refined 0.222
r_bond_other_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3524
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 396

Software

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