X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.3
Details PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.1 M SODIUM CITRATE BUFFER, PH 5.3, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.19 α = 90
b = 102.05 β = 90
c = 145.06 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH PREMIRROR, BENT MIRROR 2002-07-01
Diffraction Radiation
Monochromator Protocol
TRIANGULAR MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, HAMBURG BW7B

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
2 40 96.9 -- 0.047 -- 4.2 -- 38821 -- -- --
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)
2.0 2.2 96.1 -- 0.332 3.4 4.0 --

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 2.0 72.55 -- -- -- 36850 1933 96.8 -- 0.223 0.221 0.259 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 2.0 2.05 -- 127 2654 0.286 0.355 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.93
Anisotropic B[1][1] 4.8
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.59
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.504
r_scbond_it 2.739
r_mcangle_it 1.554
r_mcbond_it 0.913
r_nbd_refined 0.235
r_gen_planes_other 0.004
r_gen_planes_refined 0.008
r_chiral_restr 0.118
r_dihedral_angle_3_deg 18.816
r_dihedral_angle_1_deg 4.963
r_angle_other_deg 0.901
r_angle_refined_deg 1.945
r_bond_other_d 0.001
r_bond_refined_d 0.021
r_nbd_other 0.216
r_xyhbond_nbd_refined 0.133
r_xyhbond_nbd_other 0.096
r_symmetry_vdw_refined 0.397
r_symmetry_vdw_other 0.245
r_symmetry_hbond_refined 0.227
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3576
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 62

Software

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