2QIK | pdb_00002qik

Crystal structure of YkqA from Bacillus subtilis. Northeast Structural Genomics Target SR631

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL		277	0.1 M NaCl, 0.1 Na Citrate, 60% PEG 400, MICROBATCH UNDER OIL, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.9125	35.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.577	α = 90
b = 62.131	β = 101.69
c = 55.527	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	CCD	ADSC QUANTUM 4	mirrors	2007-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97900	NSLS	X4A

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	1.35	50	99	0.041	18.8	3.8		55141		-3

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)
	1.35	1.4	99.7		0.179		3.6	11083

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	SAD	THROUGHOUT	1.35	19.35	55139	2801	97.83	0.133	0.131	0.2125	0.176	0.2327	RANDOM	12.597

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]
0.07		-0.17	-0.22		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.399
r_sphericity_free	16.723
r_dihedral_angle_4_deg	14.389
r_dihedral_angle_3_deg	13.158
r_scangle_it	6.405
r_dihedral_angle_1_deg	6.376
r_sphericity_bonded	5.757
r_scbond_it	5.173
r_mcangle_it	3.506
r_mcbond_it	3.04
r_rigid_bond_restr	2.515
r_angle_refined_deg	2.056
r_angle_other_deg	0.973
r_mcbond_other	0.968
r_symmetry_vdw_refined	0.32
r_symmetry_vdw_other	0.299
r_nbd_refined	0.229
r_nbd_other	0.21
r_nbtor_refined	0.197
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.145
r_nbtor_other	0.09
r_bond_refined_d	0.025
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2227
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling