2EKY | pdb_00002eky

Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7	295	50%(v/v) PEG200, 0.1M Tris, pH 7.0, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.437	α = 90
b = 61.394	β = 108.8
c = 87.811	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	RIGAKU RAXIS VII	mirrors	2007-02-05	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS VII	mirrors	2007-02-26	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	30	98.8	0.073	0.065	9.7	5.3	68040	68040	-3	-3	17.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.8	1.86	92.6		0.503	0.439	3.3	4.8	6325

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 1LXN	1.8	30	67958	67958	3418	98.7	0.194	0.192	0.192	0.19	0.232	0.23	RANDOM	23.6

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]
-1.76		-2.1	0.58		1.18

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.8
c_scangle_it	3.22
c_scbond_it	2.15
c_mcangle_it	1.98
c_mcbond_it	1.31
c_angle_deg	1.1
c_improper_angle_d	0.7
c_bond_d	0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6130
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing