X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.3
Temperature 295.0
Details 20% PEG 8000, citrate-phosphate buffer 0.05M, tris.HCl, 0.2% sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.9 α = 90
b = 137.53 β = 95.48
c = 61.88 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Focusing mirrors 1997-11-15
Diffraction Radiation
Monochromator Protocol
Focussing mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.15 40 0.988 0.079 -- -- 2.0 50978 50343 0.0 0.0 34.02
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)
2.15 2.23 0.993 0.346 -- 2.14 2.0 5046

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 2.15 10.0 -- 0.0 49989 47446 2543 99.08 0.1887 0.1887 0.1863 0.2326 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 2.15 2.203 3394 170 3394 0.225 0.287 -- 0.992
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic thermal model
Mean Isotropic B 26.82
Anisotropic B[1][1] 0.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.97
Anisotropic B[2][2] 0.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.36
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.163
r_bond_refined_d 0.016
r_angle_refined_deg 1.979
r_dihedral_angle_1_deg 7.451
r_chiral_restr 0.13
r_gen_planes_refined 0.011
r_nbd_refined 0.161
r_xyhbond_nbd_refined 0.202
r_symmetry_vdw_refined 0.148
r_symmetry_hbond_refined 0.298
r_mcbond_it 0.929
r_mcangle_it 1.652
r_scbond_it 2.902
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6799
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 494

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CCP4 V. 4.2.1 (MOLREP) Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement