3QHT

Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FNA	PDB ENTRIES 1FNA AND 2EKE
experimental model	PDB	2EKE	PDB ENTRIES 1FNA AND 2EKE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	292	14% PEG8000, 16% glycerol, pH 8.0, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.637	α = 90
b = 175.462	β = 90
c = 52.83	γ = 90

Symmetry
Space Group	P 21 21 2

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 225 mm CCD		2009-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

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	2.4	50	100	0.085	18.9	7.1	22586	22586

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	2.395	2.457	96.29		0.643	2.15	6.6

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1FNA AND 2EKE	2.4	20	21341	21341	1151	99.74	0.22558	0.22558	0.2231	0.27158	RANDOM	49.816

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]
-0.67			-0.03		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.575
r_dihedral_angle_3_deg	19.323
r_dihedral_angle_4_deg	18.328
r_dihedral_angle_1_deg	7.806
r_scangle_it	3.918
r_scbond_it	2.568
r_mcangle_it	1.923
r_angle_refined_deg	1.864
r_mcbond_it	1.107
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.27
r_nbd_refined	0.232
r_chiral_restr	0.16
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.14
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2666
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MD2	data collection
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling