3LKY | pdb_00003lky

Monomeric Griffithsin with a Single Gly-Ser Insertion

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	0.1 M sodium acetate, 0.15 M ammonium sulfate, 25% w/v PEG 3350, pH 4.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.6	α = 90
b = 48.6	β = 90
c = 94.2	γ = 120

Symmetry
Space Group	P 61

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		2009-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	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	1.1	30	97.9	0.063	13.7	6.2		48948

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	1.12	99.7		0.583		3.5	2485

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2HYR	1.11	25.17	2	48896	47848	1048	97.9	0.159	0.159	0.17	0.159	0.16	RANDOM	16.782

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]
0.09	0.05		0.09		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.015
r_dihedral_angle_4_deg	19.295
r_dihedral_angle_3_deg	11.516
r_dihedral_angle_1_deg	7.524
r_sphericity_bonded	6.104
r_scangle_it	4.965
r_scbond_it	4.218
r_mcangle_it	2.914
r_mcbond_it	2.442
r_rigid_bond_restr	2.396
r_angle_refined_deg	1.967
r_mcbond_other	1.867
r_angle_other_deg	1.013
r_symmetry_vdw_other	0.295
r_symmetry_vdw_refined	0.222
r_nbd_other	0.204
r_nbtor_refined	0.181
r_nbd_refined	0.167
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.12
r_nbtor_other	0.094
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	906
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	41

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling