X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 292.0
Details 23-26% PEG 4000, 20% GLYCEROL, 100mM AMMONIUM ACETATE, 100mM SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 26.53 α = 90
b = 56.99 β = 99.16
c = 30.95 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
IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2002-06-04
Diffraction Radiation
Monochromator Protocol
NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
1.88 30.6 95.0 0.028 0.028 -- 3.73 7196 7068 0.0 -3.0 13.0
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)
1.88 1.95 90.2 0.096 0.096 13.3 3.34 660

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 1.88 30.57 0.0 0.0 7068 6738 330 95.0 0.169 0.169 0.1668 0.2159 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 1.88 1.929 -- 19 451 0.169 0.297 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.168
Anisotropic B[1][1] -0.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.24
Anisotropic B[2][2] 0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.323
r_scbond_it 3.033
r_mcangle_it 1.828
r_mcbond_it 0.977
r_symmetry_hbond_refined 0.171
r_symmetry_vdw_other 0.346
r_symmetry_vdw_refined 0.161
r_bond_refined_d 0.017
r_bond_other_d 0.002
r_angle_refined_deg 1.579
r_angle_other_deg 0.83
r_dihedral_angle_1_deg 6.462
r_chiral_restr 0.088
r_gen_planes_refined 0.006
r_gen_planes_other 0.005
r_nbd_refined 0.22
r_nbd_other 0.258
r_nbtor_other 0.087
r_xyhbond_nbd_refined 0.184
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 763
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 72

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection