X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 2
Details CRYSTALLIZED BY BATCH METHODS FROM A 30 MG/ML SOLUTION OF GRAMICIDIN D IN GLACIAL ACETIC ACID, PH 2.0, BATCH METHOD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 20.58 α = 90
b = 27.91 β = 90
c = 52.04 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II COLLIMATOR 1998-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
1.7 100 95.0 0.05 0.05 -- 3.4 -- 11715 -- -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)
1.7 1.76 58.8 0.125 0.125 3.5 1.0 --

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
MOLECULAR REPLACEMENT 1.7 100.0 -- 0.0 3416 -- 159 95.0 0.18 0.168 -- 0.243 5% OF REFLECTIONS IN THIN RESOLUTION SHELLS.
RMS Deviations
Key Refinement Restraint Deviation
s_similar_adp_cmpnt 0.043
s_non_zero_chiral_vol 0.054
s_zero_chiral_vol 0.045
s_from_restr_planes 0.237
s_angle_d 0.024
s_bond_d 0.007
Coordinate Error
Parameter Value
Number Disordered Residues 7.0
Occupancy Sum Hydrogen 292.0
Occupancy Sum Non Hydrogen 316.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 272
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 22

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
SHELXL-97 Structure Refinement
Software
Software Name Purpose
SHELXL-97 refinement
AMORE model building