2R0K | pdb_00002r0k

Protease domain of HGFA with inhibitor Fab58

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YBW	pdb 1YBW, pdb 1FVD
experimental model	PDB	1FVD	pdb 1YBW, pdb 1FVD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5		1:1 mixture of protein complex solution and reservoir containing 1.0M K/Na tartrate, CHES pH9.5, 0.2M Lithium Sulfate, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.658	α = 90
b = 75.61	β = 92.67
c = 69.139	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	CCD	ADSC QUANTUM 315		2007-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	3.5	50	88	0.128	6.8	2.8	10827	10827		-2	9

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	3.5	3.63	85.5		0.3	2.5	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1YBW, pdb 1FVD	3.51	50	-2	10827	10827	526	87.66	0.254	0.25354	0.25056	0.2584	0.31197	0.3119	RANDOM	16.411

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]
-1.59		2.9	-0.39		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.584
r_dihedral_angle_4_deg	19.68
r_dihedral_angle_3_deg	17.899
r_dihedral_angle_1_deg	6.159
r_mcangle_it	3.276
r_scangle_it	2.463
r_mcbond_it	1.907
r_scbond_it	1.544
r_angle_refined_deg	1.19
r_symmetry_hbond_refined	0.462
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.267
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5042
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing