2YXL | pdb_00002yxl

Crystal Structure of PH0851

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SQF	PDB ENTRY 1SQF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	1.14M Na-Citrate, 0.08M Na-Hepes(pH 7.0), 8% 1.6-Hexanediol, 200mM NaCl, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.621	α = 90
b = 116.621	β = 90
c = 93.684	γ = 120

Symmetry
Space Group	P 32 2 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	Monochromator	2006-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

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	2.2	50	99.4	0.071	0.071	32.4	10.4		37661		-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	2.2	2.28	98.7		0.803	0.803	2.14	6.4	3673

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SQF	2.55	38.18	22998	1204	99.32	0.2139	0.2123	0.21	0.24575	0.24	RANDOM	37.171

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]
-0.9	-0.45		-0.9		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.787
r_dihedral_angle_3_deg	16.637
r_dihedral_angle_4_deg	13.581
r_dihedral_angle_1_deg	5.592
r_angle_refined_deg	1.113
r_scangle_it	0.76
r_scbond_it	0.459
r_mcangle_it	0.429
r_nbtor_refined	0.301
r_mcbond_it	0.24
r_nbd_refined	0.175
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_refined	0.117
r_symmetry_vdw_refined	0.11
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3574
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing