4LAM | pdb_00004lam

Crystal structure of Cordyceps militaris IDCase D323N mutant in complex with 5-carboxyl-uracil

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop	8.5	289	25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, sitting drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.361	α = 90
b = 77.361	β = 90
c = 134.421	γ = 90

Symmetry
Space Group	P 41

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	RAYONIX MX225HE		2013-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

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	2.1	50	99.9	0.085	11.7	3.8		46222

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	2.1	2.18	100		0.232		3.8	4573

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	4HK5	2.1	38.8	46175	2340	99.67	0.1609	0.1593	0.16	0.19	0.19	RANDOM	32.6788

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]
0.14			0.14		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.405
r_sphericity_free	16.45
r_dihedral_angle_4_deg	14.077
r_dihedral_angle_3_deg	13.425
r_sphericity_bonded	11.391
r_dihedral_angle_1_deg	4.997
r_rigid_bond_restr	2.448
r_mcbond_it	1.527
r_mcbond_other	1.527
r_mcangle_it	1.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.405
r_sphericity_free	16.45
r_dihedral_angle_4_deg	14.077
r_dihedral_angle_3_deg	13.425
r_sphericity_bonded	11.391
r_dihedral_angle_1_deg	4.997
r_rigid_bond_restr	2.448
r_mcbond_it	1.527
r_mcbond_other	1.527
r_mcangle_it	1.524
r_angle_other_deg	1.468
r_angle_refined_deg	1.083
r_chiral_restr	0.062
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5590
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	70

Software

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