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 PEG 8000, citrate-phosphate buffer, tris HCl, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.64 α = 90
b = 136.96 β = 95.48
c = 61.8 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 2002-01-15
Diffraction Radiation
Monochromator Protocol
-- 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
2.1 50 0.963 0.086 -- -- 2.0 54294 52285 0.0 0.0 37.7
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)
2.1 2.18 86.2 0.471 -- 1.36 2.0 4668

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 2.1 50.0 -- 0.0 52281 49622 2659 96.3 0.192 0.192 0.189 0.245 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 2.1 2.154 3204 189 3204 0.297 0.393 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic thermal model
Mean Isotropic B 31.753
Anisotropic B[1][1] 1.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.73
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.21
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 7.579
r_symmetry_vdw_refined 0.203
r_mcangle_it 2.631
r_bond_refined_d 0.016
r_scangle_it 2.664
r_xyhbond_nbd_refined 0.203
r_mcbond_it 1.589
r_chiral_restr 0.136
r_nbd_refined 0.177
r_gen_planes_refined 0.01
r_symmetry_hbond_refined 0.258
r_scbond_it 1.893
r_angle_refined_deg 2.051
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.304
Luzzati Resolution Cutoff (Low) 8.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6778
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 463

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CCP4 (MOLREP) Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
R-AXIS data collection
SCALEPACK data reduction
MOLREP version: from CCP4 model building