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
MOLECULAR REPLACEMENT 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_angle_other_deg 0.805
r_nbd_other 0.217
r_symmetry_vdw_other 0.226
r_symmetry_hbond_refined 0.223
r_xyhbond_nbd_other 0.381
r_dihedral_angle_1_deg 4.584
r_mcbond_it 0.581
r_metal_ion_refined 0.232
r_angle_refined_deg 1.657
r_gen_planes_other 0.003
r_bond_other_d 0.001
r_gen_planes_refined 0.008
r_nbd_refined 0.332
r_xyhbond_nbd_refined 0.209
r_symmetry_hbond_other 0.02
r_scbond_it 1.673
r_mcangle_it 1.057
r_bond_refined_d 0.01
r_chiral_restr 0.151
r_symmetry_vdw_refined 0.361
r_dihedral_angle_3_deg 16.142
r_scangle_it 2.829
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

Software
Software Name Purpose
REFMAC refinement version: 5.0.32
DENZO data reduction
SCALEPACK data scaling
CNS phasing