4FBJ

Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in complex with human Nedd8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GQJ	PDB ENTRIES 3GQJ and 1NDD
experimental model	PDB	1NDD	PDB ENTRIES 3GQJ and 1NDD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	289	20% PEG 4000, 200mM sodium acetate, 100mM MES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.73	α = 90
b = 56.09	β = 104.13
c = 67.55	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315r		2011-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.91340	Diamond	I02

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	1.6	42.6	96.4	0.052	11.5	4.4	39093	39093	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	96.2		0.288	3	4.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3GQJ and 1NDD	1.6	38.2	39093	35599	1881	95.87	0.16848	0.16485	0.23624	RANDOM	23.474

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]
0.21		-0.43	-0.46		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.814
r_dihedral_angle_4_deg	16.983
r_dihedral_angle_3_deg	14.651
r_scangle_it	7.642
r_dihedral_angle_1_deg	6.873
r_scbond_it	5.333
r_mcangle_it	3.628
r_rigid_bond_restr	2.829
r_mcbond_it	2.413
r_angle_refined_deg	2.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.814
r_dihedral_angle_4_deg	16.983
r_dihedral_angle_3_deg	14.651
r_scangle_it	7.642
r_dihedral_angle_1_deg	6.873
r_scbond_it	5.333
r_mcangle_it	3.628
r_rigid_bond_restr	2.829
r_mcbond_it	2.413
r_angle_refined_deg	2.047
r_chiral_restr	0.143
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2586
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	1

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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 R01GM133198.