X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XNMPDB ENTRY 1XNM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5296PEG 3350, SODIUM ACETATE, TRIS-HCL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.652.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.157α = 91.11
b = 41.867β = 92.73
c = 97.795γ = 107.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.520960.0893.220190-361
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.696.60.3883.23.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD WITH SEMI-BRUTE- FORCE MOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XNM2.52019157104096.20.2770.2730.349RANDOM61.39
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-2.31.34-5.880.74-0.691.76
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it9.684
r_mcangle_it8.38
r_scbond_it6.774
r_mcbond_it6.269
r_dihedral_angle_1_deg6.104
r_angle_other_deg3.65
r_angle_refined_deg1.526
r_symmetry_vdw_other0.286
r_nbd_other0.259
r_nbd_refined0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it9.684
r_mcangle_it8.38
r_scbond_it6.774
r_mcbond_it6.269
r_dihedral_angle_1_deg6.104
r_angle_other_deg3.65
r_angle_refined_deg1.526
r_symmetry_vdw_other0.286
r_nbd_other0.259
r_nbd_refined0.233
r_xyhbond_nbd_refined0.192
r_symmetry_vdw_refined0.189
r_symmetry_hbond_refined0.131
r_nbtor_other0.104
r_chiral_restr0.071
r_bond_refined_d0.016
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4145
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata scaling
XDSdata reduction
SHELXDphasing
MOLEMAN2model building
REFMACrefinement
MOLEMAN2phasing