4KXP | pdb_00004kxp

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant I10D in T-state

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	PEG 3350, t-butyl alcohol, 2-methyl-2,4-pentanediol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.544	α = 90
b = 166.382	β = 90
c = 78.946	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.7	36.09	85.3	0.091	8.2	2.38	22303	19025	2	5

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	2.7	2.8	84.1		0.269	3	2.3	1819

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.7	35.66	22303	18998	979	85.18	0.2068	0.2043	0.22	0.2516	0.25	RANDOM	24.9342

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]
-0.01			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.251
r_dihedral_angle_4_deg	20.165
r_dihedral_angle_3_deg	17.091
r_dihedral_angle_1_deg	3.82
r_scangle_it	3.532
r_scbond_it	2.164
r_angle_refined_deg	1.551
r_mcangle_it	1.543
r_mcbond_it	0.839
r_chiral_restr	0.151

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.251
r_dihedral_angle_4_deg	20.165
r_dihedral_angle_3_deg	17.091
r_dihedral_angle_1_deg	3.82
r_scangle_it	3.532
r_scbond_it	2.164
r_angle_refined_deg	1.551
r_mcangle_it	1.543
r_mcbond_it	0.839
r_chiral_restr	0.151
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4744
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	92

Software

Software
Software Name	Purpose
d*TREK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data scaling
MOLREP	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.