3TJU | pdb_00003tju

Crystal structure of human granzyme H with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TK9	PDB ENTRY 3TK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	0.2M Li2SO4, 0.1M Bicine (pH 8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.239	α = 90
b = 63.239	β = 90
c = 144.782	γ = 90

Symmetry
Space Group	P 41 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 270		2010-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

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	2.7	50	99.4	0.099	58.5	35.5	8741	8689		-0.5	50.6

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	2.7	2.8	99.6		0.248	12.7	22.2	843

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 3TK9	2.7	50	8604	406	99.69	0.232	0.2294	0.2257	0.2885	0.2835	RANDOM	34.7543

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]
4.24			4.24		-8.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.785
r_dihedral_angle_3_deg	19.409
r_dihedral_angle_4_deg	16.806
r_dihedral_angle_1_deg	6.391
r_scangle_it	2.765
r_scbond_it	1.665
r_angle_refined_deg	1.59
r_mcangle_it	1.031
r_mcbond_it	0.549
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1796
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	15

Software

Software
Software Name	Purpose
ADSC	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing