X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 292.0
Details 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL DROPS OF THE PROTEIN SOLUTION WERE MIXED WITH 2 UL OF RESERVOIR SOLUTION CONTAINING 2% PEG 400, 2 M AMMONIUM SULFATE AND 0.1 M NA HEPES, PH 7.5. THE HANGING DROPLETS WERE EQUILIBRATED AT 19 DEG C THROUGH THE GAS PHASE WITH THE RESERVOIR. PRISMATIC CRYSTALS MEASURING UP TO 0.4 MM GREW WITHIN 12 HOURS. FOR LOW-TEMPERATURE DATA COLLECTION (100 K), THE CRYSTAL WAS CRYOPROTECTED IN THE RESERVOIR SOLUTION SUPPLEMENTED BY 30 % ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.89 α = 90
b = 51.89 β = 90
c = 43.03 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-07-07
Diffraction Radiation
Monochromator Protocol
SI SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 -- EMBL/DESY, Hamburg X11

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
0.86 20 94.9 0.036 -- -- 17.3 -- 47018 -- -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)
0.86 0.9 88.6 0.488 -- 3.61 6.0 --

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
EXISTING MODEL 0.86 10.0 -- -- 46998 -- 1883 94.9 0.1072 0.1068 -- 0.14 RANDOM
RMS Deviations
Key Refinement Restraint Deviation
s_bond_d 0.023
s_zero_chiral_vol 0.06
s_anti_bump_dis_restr 0.081
s_rigid_bond_adp_cmpnt 0.007
s_angle_d 0.043
s_non_zero_chiral_vol 0.083
s_approx_iso_adps 0.094
s_from_restr_planes 0.035
s_similar_adp_cmpnt 0.041
Coordinate Error
Parameter Value
Number Disordered Residues 12.0
Occupancy Sum Hydrogen 426.0
Occupancy Sum Non Hydrogen 603.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 452
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 170

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHELX model building
SHELXL-97 refinement
SHELX phasing