2QT4 | pdb_00002qt4

Atomic-resolution crystal structure of the natural form of Scytovirin

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	293	30% PEG 8000, 0.2M Li2SO4, 0.1M Na Acetate, pH 4.7, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.48	α = 90
b = 38.84	β = 90
c = 59.72	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	ADSC QUANTUM 210		2002-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	0.979	NSLS	X9B

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	1.3	25	99.2	0.082	12.3	5.6		21876

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.35	95.8			4.5	2080

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	SAD	THROUGHOUT	1.3	19.42	20294	939	92.87	0.147	0.145	0.15	0.198	0.2	RANDOM	12.744

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]
0.07			0.33		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.363
r_dihedral_angle_3_deg	11.322
r_dihedral_angle_1_deg	6.512
r_sphericity_bonded	6.3
r_dihedral_angle_4_deg	5.33
r_scangle_it	4.426
r_scbond_it	4.242
r_mcangle_it	4.016
r_mcbond_it	3.532
r_rigid_bond_restr	3.105
r_mcbond_other	1.739
r_angle_refined_deg	1.525
r_angle_other_deg	1.035
r_symmetry_vdw_other	0.271
r_xyhbond_nbd_refined	0.227
r_nbd_refined	0.206
r_nbd_other	0.206
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.149
r_symmetry_vdw_refined	0.142
r_chiral_restr	0.1
r_nbtor_other	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	699
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms

Software

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