X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 14% PEG4000, 0.15M NAAC, 0.1M IMIDAZOLE PH 7.5, 10MM MG-UDP, 10MM G6P

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.61 α = 90
b = 125.4 β = 90
c = 176.61 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 ADSC -- 2001-11-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- 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
2.45 20 99.9 0.056 -- -- 2.8 -- 86205 -- -- --
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)
2.45 2.54 99.5 0.436 -- 2.4 2.3 --

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 2.43 100.0 -- -- -- 81873 4320 99.3 -- 0.207 0.206 0.228 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 2.44 2.5 -- 292 5728 0.284 0.321 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.54
Anisotropic B[1][1] -0.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.47
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.087
r_scbond_it 2.037
r_mcangle_it 0.948
r_mcbond_it 0.502
r_nbd_refined 0.23
r_gen_planes_refined 0.007
r_chiral_restr 0.145
r_dihedral_angle_1_deg 6.415
r_angle_refined_deg 1.81
r_bond_refined_d 0.019
r_xyhbond_nbd_refined 0.154
r_symmetry_vdw_refined 0.466
r_symmetry_hbond_refined 0.523
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14606
Nucleic Acid Atoms 0
Heterogen Atoms 184
Solvent Atoms 288

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement