4MX1 | pdb_00004mx1

Structure of ricin A chain bound with 2-amino-4-oxo-N-(2-(3-phenylureido)ethyl)-3,4-dihydropteridine-7-carboxamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RTC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.102	α = 90
b = 68.102	β = 90
c = 140.532	γ = 90

Symmetry
Space Group	P 41 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	CCD	ADSC QUANTUM 315		2012-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97648	ALS	5.0.3

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	1.59	50	99.9	0.087	9.6	14.1		45334

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	1.59	1.62	100		0.682		12.5	2217

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	1RTC	1.59	50	45227	2278	99.85	0.2285	0.2268	0.22	0.2609	0.26	RANDOM	24.7573

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]
0.63			0.63		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_4_deg	18.817
r_dihedral_angle_3_deg	17.543
r_dihedral_angle_1_deg	6.581
r_scangle_it	6.131
r_scbond_it	3.979
r_mcangle_it	2.587
r_angle_refined_deg	2.49
r_mcbond_it	1.599
r_chiral_restr	0.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_4_deg	18.817
r_dihedral_angle_3_deg	17.543
r_dihedral_angle_1_deg	6.581
r_scangle_it	6.131
r_scbond_it	3.979
r_mcangle_it	2.587
r_angle_refined_deg	2.49
r_mcbond_it	1.599
r_chiral_restr	0.336
r_bond_refined_d	0.029
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2122
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	46

Software

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