2IMH | pdb_00002imh

Crystal structure of protein SPO2555 from Silicibacter pomeroyi, Pfam DUF1028

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	560mM tri-Sodium Citrate dihydrate, pH 7, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.25	α = 90
b = 69.594	β = 90
c = 105.792	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	77	CCD	ADSC QUANTUM 315		2006-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97911	NSLS	X29A

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	1.57	20	82.7	0.093	0.093	15.4	7.1	62233	51467			17.3

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	1.57	1.66	27.4		0.44	0.044	1.4	1.8	8896

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.57	20	59107	48829	2615	82.61	0.17253	0.17076	0.2066	0.2082	RANDOM	22.771

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]
-0.66			1.95		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.117
r_dihedral_angle_4_deg	15
r_dihedral_angle_3_deg	11.289
r_dihedral_angle_1_deg	7.257
r_scangle_it	3.252
r_scbond_it	2.236
r_angle_refined_deg	1.298
r_mcangle_it	1.134
r_mcbond_it	0.943
r_nbtor_refined	0.299
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.14
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3266
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing