X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop Streak Seeding
pH 5.2
Details PROTEIN WAS CRYSTALLIZED BY HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIRS OF 1.0 M NH4(SO4)2, 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, STARTING WITH 6 MICROLITERS OF PROTEIN AT 2 MG/ML IN 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, 5 MM DTT, AND 4 MICROLITERS RESERVOIR SOLUTION. THESE DROPS OF MUTANT PROTEIN WERE STREAK-SEEDED FROM STOCKS GENERATED FROM CRUSHED DIFFRACTION-QUALITY WILD-TYPE COLICIN IA CRYSTALS. CRYSTALS WERE HARVESTED TO 1.1 M NA2SO4, 200 MM NACL, 20 MM NA-CITRATE (PH 5.2), AND 5 MM DTT. FOR DERIVATIZATION, CRYSTALS WERE WASHED IN DTT-FREE HARVEST BUFFER AND SOAKED FOR ONE WEEK IN 1 MM CH3HGCL., vapor diffusion - hanging drop - streak seeding

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.4 α = 90
b = 178.6 β = 90
c = 285.5 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate PT-COATED FUSED SILICA MIRROR 1994-04
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 -- SSRL BL7-1

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
3 25 84.0 0.13 0.13 -- 3.4 -- 28266 -- 0.0 --
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)
3.0 3.11 73.0 0.309 0.309 1.7 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
MIR 3.0 8.0 -- 0.0 -- 28260 2000 84.1 -- 0.241 0.241 0.312 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 3.0 3.1 -- 169 2117 0.373 0.392 0.03 73.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model INDIVIDUAL RESTRAINED
Mean Isotropic B 66.5
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.009
x_dihedral_angle_d 19.34
x_scangle_it 2.0
x_mcbond_it 1.5
x_improper_angle_d 1.53
x_angle_deg 1.48
x_scbond_it 2.0
x_mcangle_it 1.5
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 25.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4714
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
PHASES phasing
SOLOMON phasing
X-PLOR model building version: 3.1
XTALVIEW refinement
X-PLOR refinement version: 3.1
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing version: 3.1