4QAN | pdb_00004qan

Crystal structure of a cystatin-like protein (RUMGNA_02398) from Ruminococcus gnavus ATCC 29149 at 2.10 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M magnesium formate, 20.0% polyethylene glycol 3350, The additive is 0.1 M Cesium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.394	α = 90
b = 109.013	β = 90
c = 137.307	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	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2014-03-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.9798,0.97917	SSRL	BL11-1

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	2.1	29.671	96.2	0.085	11			45198		-3	35.714

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	2.1	2.17	93.5		0.829	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.1	29.671	45054	2271	98.05	0.1937	0.1913	0.2	0.2404	0.25	RANDOM	50.8766

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]
-1.75			-2.56		4.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.167
r_dihedral_angle_4_deg	17.482
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	5.964
r_mcangle_it	3.872
r_mcbond_it	2.61
r_mcbond_other	2.608
r_angle_refined_deg	1.224
r_angle_other_deg	0.698
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.167
r_dihedral_angle_4_deg	17.482
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	5.964
r_mcangle_it	3.872
r_mcbond_it	2.61
r_mcbond_other	2.608
r_angle_refined_deg	1.224
r_angle_other_deg	0.698
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5993
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.