X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details Protein at 12-25 mg/ml in 0.0125 M tris(hydroxymethyl)amino methane (TRIS) pH 8.0, 0.50 M NaCl; precipitating solution: 20% (w/v) PEG 3350, 0.10 M 2-(N-Morpholino)ethanesulfonic acid (MES) pH 6.5, 0.20 M potassium thiocyanate (KSCN), VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.57 α = 90
b = 71.27 β = 106.56
c = 54.6 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 parabolic collimating mirror 2001-04-13
Diffraction Radiation
Monochromator Protocol
double-crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 0.9640, 0.9796, 0.9797 NSLS X8C

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
1.5 20 99.6 0.052 0.052 -- 5.4 40628 40466 1.0 0.0 14.7
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)
1.5 1.57 100.0 0.139 0.139 5.0 5.4 5891

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 1.5 20.0 -- 0.0 40628 40466 2026 99.58 0.1806 0.1806 0.17911 0.20984 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 1.5 1.539 2816 140 2816 0.19 0.227 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model BABINET MODEL WITH MASK
Mean Isotropic B 13.834
Anisotropic B[1][1] 0.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.22
Anisotropic B[2][2] 0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.78
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.526
r_scbond_it 2.945
r_mcangle_it 1.771
r_mcbond_it 1.03
r_symmetry_hbond_refined 0.142
r_symmetry_vdw_other 0.265
r_symmetry_vdw_refined 0.3
r_xyhbond_nbd_other 0.037
r_xyhbond_nbd_refined 0.145
r_bond_refined_d 0.02
r_bond_other_d 0.001
r_angle_refined_deg 1.65
r_angle_other_deg 1.834
r_dihedral_angle_1_deg 4.546
r_dihedral_angle_3_deg 12.756
r_chiral_restr 0.105
r_gen_planes_refined 0.007
r_gen_planes_other 0.002
r_nbd_refined 0.232
r_nbd_other 0.194
r_nbtor_other 0.197
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1774
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 206

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SOLVE model building