2YKD | pdb_00002ykd

Structure of the matrix protein from human respiratory syncytial virus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VQPPDB ENTRY 2VQP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17291MOTHER LIQUOR 45 % TO 65% TACSIMATE PH7, 18 DEGC, PROTEIN AT 1 MG/ML
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.402α = 90
b = 78.902β = 96.18
c = 65.827γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8525.2980.087.13.722370120.95
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.95980.511.33.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VQP1.8625.1921102109599.230.18210.17960.180.228790.23RANDOM23.769
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]
-0.130.010.17-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.361
r_dihedral_angle_4_deg23.259
r_dihedral_angle_3_deg14.784
r_dihedral_angle_1_deg6.351
r_scangle_it4.401
r_scbond_it3.139
r_mcangle_it1.879
r_angle_refined_deg1.658
r_mcbond_it1.584
r_nbtor_refined0.311
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1996
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing