3EJ5 | pdb_00003ej5

complex of Ricin A chain and pyrimidine-based inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.9	277	tris-HCl, BME, EDTA, PEG 8000, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.642	α = 90
b = 68.006	β = 112.97
c = 49.675	γ = 90

Symmetry
Space Group	P 1 21 1

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	varimax	2008-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	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	2.5	30	99.8	0.044		3.4		9083

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	2.5	2.59	99.8		0.113		3.1	893

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		THROUGHOUT	PDB entry 1RTC	2.5	25.7	8936	467	98.18	0.198	0.194	0.2	0.266	0.2	RANDOM	25.539

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]
-1.62		-1.09	0.33		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.865
r_dihedral_angle_4_deg	18.502
r_dihedral_angle_3_deg	15.084
r_dihedral_angle_1_deg	5.284
r_scangle_it	5.066
r_scbond_it	3.634
r_mcangle_it	2.19
r_mcbond_it	1.373
r_angle_refined_deg	1.237
r_angle_other_deg	0.882
r_mcbond_other	0.25
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.211
r_nbd_other	0.195
r_symmetry_vdw_other	0.19
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.156
r_nbtor_other	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2024
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	21

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
MOLREP	phasing