Experiment: 3IVU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Homocitrate Synthase Lys4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	297	Na/KPO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.798	α = 90
b = 133.798	β = 90
c = 125.657	γ = 120

Symmetry
Space Group	P 62

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		2007-12-08	M	SINGLE WAVELENGTH

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

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	2.72	40	96.4	0.056	12.3	3.8	33176	33176		-3

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	2.72	2.82	98.5		0.495	2.54	3.7	3362

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Homocitrate Synthase Lys4	2.72	39.41	33176	33172	1681	96.2	0.18	0.18	0.177	0.217	RANDOM	66.186

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]
-1.01	-0.5		-1.01		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.137
r_dihedral_angle_3_deg	16.764
r_dihedral_angle_4_deg	16.261
r_dihedral_angle_1_deg	6.111
r_scangle_it	3.183
r_scbond_it	1.899
r_angle_refined_deg	1.453
r_mcangle_it	1.07
r_mcbond_it	0.535
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.137
r_dihedral_angle_3_deg	16.764
r_dihedral_angle_4_deg	16.261
r_dihedral_angle_1_deg	6.111
r_scangle_it	3.183
r_scbond_it	1.899
r_angle_refined_deg	1.453
r_mcangle_it	1.07
r_mcbond_it	0.535
r_nbtor_refined	0.309
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.209
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5771
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	24

Software

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