3MLC | pdb_00003mlc

Crystal structure of FG41MSAD inactivated by 3-chloropropiolate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MJZ	PDB ENTRY 3MJZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Sitting drop	8.5	277	3 micro liter of protein solution (24.5 mg/mL in 10 mM sodium phosphate buffer, pH 8) mixed with 3 micro liter crystallization solution (0.1 M Tris hydrochloride buffer, pH 8.5, 2.0 M mono-ammonium dihydrogen phosphate), Sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.227	α = 90
b = 144.227	β = 90
c = 144.227	γ = 90

Symmetry
Space Group	P 21 3

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		2007-12-25	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	2.21	102.06	95.1	0.116	8.1	33.1		47735

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	2.21	2.29	55.9		0.894		2

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	PDB ENTRY 3MJZ	2.224	102.06	45095	2398	96.47	0.2265	0.22394	0.22	0.27504	0.27	RANDOM	38.467

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.438
r_dihedral_angle_4_deg	18.643
r_dihedral_angle_3_deg	17.983
r_dihedral_angle_1_deg	7.046
r_scangle_it	3.258
r_scbond_it	2.158
r_angle_refined_deg	1.687
r_mcangle_it	1.217
r_mcbond_it	0.733
r_nbtor_refined	0.309
r_nbd_refined	0.252
r_xyhbond_nbd_refined	0.215
r_symmetry_hbond_refined	0.201
r_symmetry_vdw_refined	0.184
r_chiral_restr	0.127
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4911
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	30

Software

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