X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.99
Temperature 293.0
Details 50mM Sodium Cacodylate buffer, 10mM MnCl2, 1mM Spermine, 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 24.61 α = 90
b = 31.26 β = 103.64
c = 31.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2007-09-15
Diffraction Radiation
Monochromator Protocol
Mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2.8 15 95.0 0.042 0.042 -- 2.88 1241 1179 -- 1.0 42.5
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)
2.8 2.87 94.8 0.129 0.1149 3.3 3.25 72

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 2.8 14.71 -- -- -- 1108 61 97.01 -- 0.16692 0.16485 0.20162 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 2.8 2.87 72 1 77 0.295 0.202 -- 95.12
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 12.018
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.896
r_scbond_it 4.122
r_nbd_refined 0.235
r_gen_planes_refined 0.023
r_chiral_restr 0.152
r_angle_refined_deg 4.456
r_bond_refined_d 0.031
r_nbtor_refined 0.341
r_xyhbond_nbd_refined 0.115
r_symmetry_vdw_refined 0.294
r_symmetry_hbond_refined 0.021
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.327
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 480
Heterogen Atoms 2
Solvent Atoms 12

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
AUTOMAR Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
PHASER model building
MAR345dtb data collection