Experiment: 1FZM

MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VAA	pdb-entry 2vaa without peptide, water, and mutated side chains truncated to alanine.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	290	K/Na phosphate, MPD , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.26	α = 90
b = 88.15	β = 90
c = 45.59	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	22.1	95.1	0.065	23.2	2.9	49672	49672		2.5	22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.82	91.9		0.48	2.5	2.5	1565

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	CNS, done by rigid body refinement of starting model.	THROUGHOUT	pdb-entry 2vaa without peptide, water, and mutated side chains truncated to alanine.	1.8	22.07	47828	3641	91.5	0.21	0.21	0.2179	0.223	0.2318	RANDOM	30.9

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]
1.85			3.22		-5.07

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.8
c_scangle_it	2.48
c_mcangle_it	1.63
c_scbond_it	1.58
c_angle_deg	1.4
c_improper_angle_d	1.12
c_mcbond_it	1.01
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3118
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	86

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing