4HJD | pdb_00004hjd

GCN4pLI derivative with alpha/beta/acyclic-gamma amino acid substitution pattern

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GCL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	0.1 M NaOAc, 8% w/v PEG4000, cryoprotected by addition of 24% PEG4000 to mother liquor, precipitant solution combined 1+1 uL with peptide stock at 10 mg/mL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.92	α = 90
b = 51.49	β = 128.87
c = 31.03	γ = 90

Symmetry
Space Group	C 1 2 1

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		2012-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.7	17.62	98.3	0.034	23.38	3.72		6350		-3	28.775

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GCL	1.7	17.62	6053	298	99.44	0.2525	0.2506	0.25	0.295	0.3	RANDOM	22.6426

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]
-0.08		-0.05	-0.82		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.199
r_sphericity_free	15.398
r_dihedral_angle_3_deg	13.038
r_dihedral_angle_4_deg	11.932
r_sphericity_bonded	4.816
r_dihedral_angle_1_deg	3.184
r_rigid_bond_restr	2.209
r_angle_other_deg	1.004
r_angle_refined_deg	0.906
r_chiral_restr	0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.199
r_sphericity_free	15.398
r_dihedral_angle_3_deg	13.038
r_dihedral_angle_4_deg	11.932
r_sphericity_bonded	4.816
r_dihedral_angle_1_deg	3.184
r_rigid_bond_restr	2.209
r_angle_other_deg	1.004
r_angle_refined_deg	0.906
r_chiral_restr	0.048
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	535
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
EMBL	data collection
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.