7XLO | pdb_00007xlo

Crystal Structure of the Catalytic Domain of Inosine Monophosphate Dehydrogenase (IMPDH) from Methanocaldococcus jannaschii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CU0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		297	0.05 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 30% v/v polyethylene glycol monomethyl ether 550

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.65	α = 90
b = 97.65	β = 90
c = 168.22	γ = 90

Symmetry
Space Group	I 4

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	MAR scanner 345 mm plate		2018-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.6	53.37	100	0.845	4	4.4		24178

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74			0.845

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	2cu0	2.6	53.37	22945	1233	99.98	0.25525	0.25416	0.26	0.27606	0.28	RANDOM	15.675

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]
-0.6			-0.6		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.029
r_dihedral_angle_3_deg	18.403
r_dihedral_angle_4_deg	14.228
r_dihedral_angle_1_deg	8.059
r_long_range_B_refined	3.173
r_long_range_B_other	3.165
r_angle_refined_deg	1.559
r_angle_other_deg	1.365
r_mcangle_it	1.336
r_mcangle_other	1.336
r_scangle_other	1.099
r_mcbond_it	0.762
r_mcbond_other	0.762
r_scbond_it	0.614
r_scbond_other	0.613
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4756
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing