3EJV

Crystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	2.0000M (NH4)2SO4, 2.0000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.54	α = 90
b = 79.54	β = 90
c = 79.54	γ = 90

Symmetry
Space Group	P 21 3

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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97929	SSRL	BL9-2

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	1.4	28.127	99.3	0.048	13.99			33205		-3	13.35

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)
	1.4	1.45	97		0.55	2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.4	28.127	33165	1672	99.87	0.143	0.142	0.161	RANDOM	16.11

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.973
r_dihedral_angle_4_deg	17.2
r_dihedral_angle_3_deg	11.86
r_dihedral_angle_1_deg	6.624
r_sphericity_free	6.287
r_sphericity_bonded	3.057
r_scangle_it	2.888
r_mcangle_it	2.606
r_scbond_it	2.131
r_mcbond_it	1.99
r_angle_refined_deg	1.545
r_rigid_bond_restr	1.363
r_angle_other_deg	0.971
r_mcbond_other	0.859
r_symmetry_vdw_other	0.295
r_nbd_refined	0.223
r_nbd_other	0.214
r_symmetry_vdw_refined	0.186
r_nbtor_refined	0.172
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.112
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1203
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing