3KQZ | pdb_00003kqz

Structure of a protease 2

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, 1mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.698	α = 90
b = 173.728	β = 90
c = 220.278	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r		2009-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95659	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.39	77.69	100	0.367	0.101	5.8	14.3		256048

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 3KQX	2.39	56.08	243011	12914	99.11	0.17924	0.17592	0.1819	0.24187	0.2463	RANDOM	27.779

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]
-2.21			-0.15		2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.657
r_dihedral_angle_4_deg	19.377
r_dihedral_angle_3_deg	16.154
r_scangle_it	8.272
r_dihedral_angle_1_deg	6.643
r_scbond_it	5.746
r_mcangle_it	3.001
r_angle_refined_deg	1.714
r_mcbond_it	1.441
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	46749
Nucleic Acid Atoms
Solvent Atoms	2523
Heterogen Atoms	790

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling