4DPO | pdb_00004dpo

Crystal structure of a conserved protein MM_1583 from Methanosarcina mazei Go1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris, pH 8.5, 2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.761	α = 90
b = 60.255	β = 90
c = 104.312	γ = 90

Symmetry
Space Group	P 21 21 21

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	Mirrors	2012-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9790	NSLS	X29A

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	2.71	50	98.7	0.06	13.8	13.7	10299	10299

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	2.71	2.81	100		0.6	5	14.5	1024

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.73	39.43	10299	9723	490	97.05	0.23826	0.23607	0.2474	0.28291	0.2747	RANDOM	58.32

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]
-0.03			-0.01		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.519
r_dihedral_angle_3_deg	21.729
r_dihedral_angle_4_deg	13.554
r_dihedral_angle_1_deg	7.177
r_scangle_it	4.806
r_scbond_it	3.067
r_angle_refined_deg	1.962
r_mcangle_it	1.858
r_mcbond_it	0.954
r_chiral_restr	0.12
r_bond_refined_d	0.022
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1549
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
AutoSol	phasing
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing