2QSK

Atomic-resolution crystal structure of the Recombinant form of Scytovirin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QT4	PDB ENTRY 2QT4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	1M sodium citrate, 0.1 M imidazole pH 8.0, protein concentration 32 MG/ML VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.2	α = 90
b = 38.79	β = 90
c = 59.87	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	MARMOSAIC 300 mm CCD		2007-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.979	APS	22-ID

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	50	98.8	0.057	19.3	4.6	48601	48018		-3

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	1	1.02	85.3		0.404	1.9	2.2	2030

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD/DIRECT REFINEMENT	THROUGHOUT	PDB ENTRY 2QT4	1	30	47944	980	98.56	0.129	0.128	0.147	RANDOM	10.18

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]
0.24			-0.12		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.829
r_sphericity_free	12.036
r_dihedral_angle_3_deg	10.879
r_dihedral_angle_4_deg	6.269
r_dihedral_angle_1_deg	5.854
r_sphericity_bonded	4.858
r_scangle_it	3.687
r_scbond_it	3.501
r_mcangle_it	3.178
r_mcbond_it	2.565
r_rigid_bond_restr	1.584
r_angle_refined_deg	1.392
r_mcbond_other	1.203
r_angle_other_deg	0.885
r_xyhbond_nbd_refined	0.26
r_symmetry_vdw_other	0.255
r_nbd_other	0.204
r_nbd_refined	0.196
r_nbtor_refined	0.17
r_symmetry_hbond_refined	0.148
r_symmetry_vdw_refined	0.132
r_nbtor_other	0.089
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	674
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	9

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SHELXS	phasing