2HYR | pdb_00002hyr

Crystal structure of a complex of griffithsin with maltose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.8M magnesium sulfate, 0.1M MES, 1:10 ratio of griffithsin monomers to maltose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.82	α = 90
b = 53.26	β = 90
c = 118.47	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		2006-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.51	50	99.9			35264	35264		-3

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	1.51	1.56	99.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2GUC	1.51	30	35264	33427	1764	99.62	0.15395	0.15395	0.15229	0.16	0.1854	0.2	RANDOM	15.097

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]
-0.46			-0.56		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.623
r_dihedral_angle_4_deg	18.967
r_dihedral_angle_3_deg	13.525
r_dihedral_angle_1_deg	7.337
r_scangle_it	4.372
r_scbond_it	3.357
r_angle_other_deg	2.841
r_mcangle_it	1.998
r_angle_refined_deg	1.959
r_mcbond_it	1.622
r_chiral_restr	0.644
r_mcbond_other	0.404
r_symmetry_vdw_refined	0.338
r_symmetry_vdw_other	0.309
r_symmetry_hbond_refined	0.284
r_nbd_refined	0.233
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.183
r_nbtor_other	0.099
r_metal_ion_refined	0.026
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1798
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	167

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
DENZO	data reduction
HKL-2000	data scaling
SCALEPACK	data scaling
PHASER	phasing