3K6J | pdb_00003k6j

Crystal structure of the dehydrogenase part of multifuctional enzyme 1 from C.elegans

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	0.1M Tris-HCl, 0.1M K2HPO4, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.025	α = 90
b = 90.657	β = 90
c = 66.206	γ = 90

Symmetry
Space Group	P 21 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	MAR CCD 165 mm		2009-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 3W1A	0.979	BSRF	3W1A

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	2.2	31.09	100	0.101	26.6	12.9	24541	24533			34.4

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)
	2.2	2.28	100		0.676	3.7	12.7	2404

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1ZCJ	2.2	31.09	24489	23225	1230	99.87	0.21256	0.21256	0.20971	0.2131	0.26734	0.2205	RANDOM	38.314

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]
-0.15			-1.44		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.543
r_dihedral_angle_3_deg	16.547
r_dihedral_angle_4_deg	11.818
r_dihedral_angle_1_deg	5.357
r_scangle_it	3.143
r_scbond_it	1.93
r_mcangle_it	1.3
r_angle_refined_deg	1.278
r_mcbond_it	0.701
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3429
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	21

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
OASIS	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
OASIS	phasing