X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details sodium formate, sodium citrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.55 α = 90
b = 64.11 β = 90
c = 73.56 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2002-10-07
Diffraction Radiation
Monochromator Protocol
confocal multilayer optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-D 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
1.5 50 97.6 0.06 -- -- 5.8 30701 30701 -- -- 17.3
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)
1.5 1.55 94.8 0.576 -- 3.1 5.5 2915

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 1.5 48.2 0.0 0.0 30657 30657 1543 97.6 0.161 0.161 0.16 0.177 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 1.5 1.539 1998 114 1998 0.385 0.426 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 13.4
Anisotropic B[1][1] 0.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.714
r_scbond_it 2.39
r_mcangle_it 1.639
r_mcbond_it 0.902
r_symmetry_hbond_refined 0.172
r_symmetry_vdw_other 0.339
r_symmetry_vdw_refined 0.278
r_bond_refined_d 0.014
r_bond_other_d 0.0
r_angle_refined_deg 1.529
r_angle_other_deg 3.781
r_dihedral_angle_1_deg 6.179
r_chiral_restr 0.106
r_gen_planes_refined 0.007
r_gen_planes_other 0.01
r_nbd_refined 0.215
r_nbd_other 0.296
r_nbtor_other 0.107
r_xyhbond_nbd_refined 0.158
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.066
Luzzati ESD (R-Free Set) 0.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1359
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 231

Software

Computing
Computing Package Purpose
CRYSTALCLEAR Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement