5C9B | pdb_00005c9b

Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	293	24% PEG4000, 0.2 M lithium sulfate, pH 5.8

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.985	α = 90
b = 101.985	β = 90
c = 127.063	γ = 120

Symmetry
Space Group	P 32 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	MARMOSAIC 300 mm CCD		2012-10-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9825	APS	22-ID

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	2.4	50	87.6	0.054	0.054	31.27	5.6	31615	28761

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	2.4	2.44	33.6		0.419	2.67	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.4	47.37	27301	1458	91.02	0.20206	0.19893	0.2	0.26222	0.26	RANDOM	72.462

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]
1.1	1.1		1.1		-3.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.24
r_long_range_B_other	20.682
r_long_range_B_refined	20.643
r_dihedral_angle_4_deg	20.563
r_scangle_other	18.544
r_dihedral_angle_3_deg	18.511
r_scbond_it	14.996
r_scbond_other	14.992
r_mcangle_other	13.07
r_mcangle_it	13.063
r_mcbond_it	10.533
r_mcbond_other	10.501
r_dihedral_angle_1_deg	7.141
r_angle_refined_deg	1.819
r_angle_other_deg	0.839
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3892
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing