X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 4 UL HANGING DROPS (2 UL OF DAPDC 10 MG/ML CONTAINING 5MM OF LYSINE COMBINED WITH 2 UL OF WELL SOLUTION) WERE EQUILIBRATED AGAINST 500 UL OF WELL SOLUTION (24% PEG-MME 5K, 0.1M MES BUFFER PH6.3 AND 60 MM AMMONIUM SULFATE). THESE CRYSTALS WERE SOAKED FOR 3 HRS IN IN MOTHER LIQUOR CONTAINING 0.2 MM PLP. THE CRYSTALS ARE DISTINCTLY YELLOW., pH 6.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.45 α = 90
b = 111.45 β = 90
c = 238.25 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC DOUBLE MONO 2002-11-15
Diffraction Radiation
Monochromator Protocol
SI SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B -- APS 14-ID-B

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
2.6 65.5 99.8 0.081 -- -- 6.2 -- 44373 -- -- --
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)
2.6 2.67 94.0 0.405 -- 3.1 6.2 --

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
MOLECULAR REPLACEMENT 2.6 18.0 -- -- -- 44373 2374 99.8 -- 0.227 0.224 0.268 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 2.6 2.67 -- 171 3160 0.392 0.38 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.48
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.15
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.474
r_scbond_it 2.805
r_mcangle_it 2.042
r_mcbond_it 1.132
r_nbd_refined 0.228
r_gen_planes_other 0.004
r_gen_planes_refined 0.006
r_chiral_restr 0.116
r_dihedral_angle_1_deg 6.95
r_angle_other_deg 0.858
r_angle_refined_deg 1.552
r_bond_other_d 0.002
r_bond_refined_d 0.03
r_nbd_other 0.259
r_nbtor_other 0.1
r_xyhbond_nbd_refined 0.186
r_symmetry_vdw_refined 0.159
r_symmetry_vdw_other 0.239
r_symmetry_hbond_refined 1.348
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6660
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 236

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
EPMR model building