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_nbd_refined 0.235
r_symmetry_hbond_refined 0.021
r_scangle_it 4.896
r_xyhbond_nbd_refined 0.115
r_bond_refined_d 0.031
r_nbtor_refined 0.341
r_chiral_restr 0.152
r_symmetry_vdw_refined 0.294
r_scbond_it 4.122
r_gen_planes_refined 0.023
r_angle_refined_deg 4.456
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

Software
Software Name Purpose
MAR345dtb data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
AUTOMAR data reduction
SCALEPACK data scaling