1BZ9 | pdb_00001bz9

CRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SYNTHETIC PEPTIDE P1027

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HOC	PDB ENTRY 1HOC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.35	α = 90
b = 109.19	β = 122.81
c = 57.78	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS	MIRRORS	1997-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.8	30	99.9	0.091	20.4	5.3		11820			46.4

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)
	2.8	2.9	100		0.292	5.9	6.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1HOC	2.8	30	11759	559	99	0.266	0.252	0.22	0.319	0.28	RANDOM	34.4

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]
0.466		8.675	-11		10.55

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	24.6
p_staggered_tor	21.4
p_scangle_it	5.236
p_mcangle_it	4.101
p_scbond_it	3.157
p_mcbond_it	2.37
p_planar_tor	2
p_multtor_nbd	0.275
p_singtor_nbd	0.18
p_xyhbond_nbd	0.152
p_chiral_restr	0.116
p_hb_or_metal_coord	0.05
p_planar_d	0.03
p_angle_d	0.027
p_plane_restr	0.0149
p_bond_d	0.009
p_angle_deg
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3147
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	phasing