1U9Q | pdb_00001u9q

Crystal structure of cruzain bound to an alpha-ketoester

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AIM	cruzipain coordinate set 1AIM, without inhibitor or water molecules

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	0.6-1M NaCitrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.96	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.72	α = 90
b = 50.675	β = 116.74
c = 45.576	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS II	Yale MSC mirrors	2000-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.3	40.82		0.092		5.1	7826	7826

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)
	2.3	2.37	88.2		0.207		2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	cruzipain coordinate set 1AIM, without inhibitor or water molecules	2.3	40.82	7826	7457	363	93.32	0.13627	0.13224	0.13	0.21773	0.22	RANDOM	14.744

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]
0.05		-0.73	0.09		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.413
r_dihedral_angle_4_deg	19.529
r_dihedral_angle_3_deg	15.443
r_dihedral_angle_1_deg	6.616
r_scangle_it	4.223
r_scbond_it	2.669
r_angle_refined_deg	1.876
r_mcangle_it	1.599
r_mcbond_it	0.988
r_nbtor_refined	0.314
r_nbd_refined	0.276
r_symmetry_vdw_refined	0.273
r_xyhbond_nbd_refined	0.186
r_symmetry_hbond_refined	0.177
r_chiral_restr	0.109
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1592
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
REFMAC	refinement
X-PLOR	phasing