X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG3000, lithium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.87 α = 90
b = 246.86 β = 90
c = 87.38 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-09-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4

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
2.4 40 97.7 0.073 -- -- 3.7 107630 105155 -999.0 -3.7 --
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)
2.4 2.53 90.2 0.331 -- 2.5 2.8 --

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 and SIRAS 2.4 40.0 -- -- 107630 101981 3123 97.37 -- 0.21653 0.21476 0.27527 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 2.4 2.462 -- 201 6602 0.291 0.361 -- 86.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.606
Anisotropic B[1][1] -1.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.09
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.103
r_scbond_it 1.944
r_mcangle_it 1.242
r_mcbond_it 0.73
r_nbd_refined 0.246
r_gen_planes_refined 0.007
r_chiral_restr 0.117
r_dihedral_angle_4_deg 20.788
r_dihedral_angle_3_deg 20.813
r_dihedral_angle_2_deg 36.478
r_dihedral_angle_1_deg 8.963
r_angle_refined_deg 1.201
r_bond_refined_d 0.012
r_nbtor_refined 0.318
r_xyhbond_nbd_refined 0.188
r_symmetry_vdw_refined 0.204
r_symmetry_hbond_refined 0.241
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17632
Nucleic Acid Atoms 0
Heterogen Atoms 146
Solvent Atoms 611

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.700 data extraction
REFMAC5 refinement