X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details PROTEIN SOLUTION: 12 MG/ML PBGS MUTANT D139N IN 50 MM K-HEPES, 10 MM MGCL2. CRYSTALLIZATION SOLUTION: 0.99 ML PROTEIN SOLUTION = 0.01 ML 2MM 5F-LA IN 50 MM K-HEPES, 10 MM MGCL2. RESERVOIR SOLUTION: 1 M NA/K-TARTRATE, 0.2M LI2SO4, 0.1 M CHES PH = 9,5. SITTING DROP: 0.003 ML CRYSTALLISATION SOLUTION + 0.003 ML RESERVOIR SOLUTION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.13 α = 90
b = 127.13 β = 90
c = 86.14 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 2001-10-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 -- MPG/DESY, HAMBURG BW6

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
1.66 20 99.9 0.116 -- -- 5.2 -- 82775 -- 3.0 --
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)
1.66 1.72 100.0 0.394 -- 4.1 4.9 --

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
OTHER 1.66 91.29 -- -- -- 78644 4131 99.1 -- -- 0.175 0.198 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 1.66 1.7 -- 295 5780 0.214 0.241 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.86
Anisotropic B[1][1] 0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.829
r_scbond_it 1.673
r_mcangle_it 1.057
r_mcbond_it 0.581
r_nbd_refined 0.332
r_gen_planes_other 0.003
r_gen_planes_refined 0.008
r_chiral_restr 0.151
r_dihedral_angle_3_deg 16.142
r_dihedral_angle_1_deg 4.584
r_angle_other_deg 0.805
r_angle_refined_deg 1.657
r_bond_other_d 0.001
r_bond_refined_d 0.01
r_nbd_other 0.217
r_xyhbond_nbd_refined 0.209
r_xyhbond_nbd_other 0.381
r_metal_ion_refined 0.232
r_symmetry_vdw_refined 0.361
r_symmetry_vdw_other 0.226
r_symmetry_hbond_refined 0.223
r_symmetry_hbond_other 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5050
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 671

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.0.32 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0.32 refinement
CNS model building