X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.3
Details PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE BUFFER PH 5.3, 0.2 M POTASSIUM SODIUM TARTRATE, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.79 α = 90
b = 66.49 β = 117.54
c = 141.24 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
MAR 345 X-RAY RESEARCH TWO MIRRORS 2000-05-15
Diffraction Radiation
Monochromator Protocol
FLAT AND N2 COOLED AND SAGITTALY BENT MONOCHROMATORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A -- ESRF BM30A

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
1.95 24 96.6 0.032 -- -- 1.83 -- 151926 -- -- --
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)
1.95 2.0 96.6 0.142 -- 5.0 1.8 --

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
SIR 1.95 24.0 -- -- -- 140398 7402 94.1 -- 0.166 0.165 0.19 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 1.95 2.0 -- 551 10293 0.2 0.237 -- --
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.489
r_scbond_it 2.667
r_mcangle_it 1.284
r_mcbond_it 0.674
r_nbd_refined 0.227
r_gen_planes_other 0.004
r_gen_planes_refined 0.007
r_chiral_restr 0.112
r_dihedral_angle_3_deg 1.117
r_angle_other_deg 1.799
r_bond_other_d 0.002
r_bond_refined_d 0.018
r_nbd_other 0.21
r_xyhbond_nbd_refined 0.157
r_xyhbond_nbd_other 0.208
r_symmetry_vdw_refined 0.153
r_symmetry_vdw_other 0.178
r_symmetry_hbond_refined 0.125
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9520
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 1213

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE, DM Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
DM model building
MLPHARE model building