3U5R | pdb_00003u5r

Crystal structure of a hypothetical protein SMc02350 from Sinorhizobium meliloti 1021

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YWI	pdb entry 2YWI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.2M Ammonium acetate, 0.1M tri sodium citrate pH 5.6, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.657	α = 82.65
b = 58.567	β = 83.58
c = 85.476	γ = 66.29

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315	mirrors	2011-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9792	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	2.05	50	97.9	0.05	13.2	4.4	59768	59768

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	2.05	2.12	96.5		0.27	5	4.3	5911

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 (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 2YWI	2.05	34.02	59768	56737	3026	97.79	0.18445	0.18192	0.1835	0.2321	0.2313	RANDOM	26.28

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]
	0.01	0.01	-0.02	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.59
r_dihedral_angle_4_deg	17.444
r_dihedral_angle_3_deg	15.987
r_dihedral_angle_1_deg	6.286
r_scangle_it	5.86
r_scbond_it	3.725
r_mcangle_it	2.226
r_angle_refined_deg	1.901
r_mcbond_it	1.242
r_chiral_restr	0.155
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5586
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling