5VZ3 | pdb_00005vz3

Growth Factor Crystal Structure at 1.97 Angstrom Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	298	25% v/v MPD, 0.1 M sodium citrate, pH 4.0, 10 mM ATP

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.964	α = 90
b = 123.02	β = 90
c = 41.698	γ = 90

Symmetry
Space Group	C 2 2 2

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		2013-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.7430	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	1.97	50	95.3	0.082	14.2	42.7		9013

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	1.97	2.04	72		0.371		8.5	656

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	1.97	41.7	8576	437	95.24	0.1961	0.1935	0.2033	0.2483	0.2525	RANDOM	52.468

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					-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.681
r_dihedral_angle_3_deg	15.523
r_dihedral_angle_4_deg	13.531
r_dihedral_angle_1_deg	6.857
r_angle_refined_deg	1.928
r_angle_other_deg	1.02
r_chiral_restr	0.111
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	826
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
SHELX	phasing
PHASER	phasing
HKL-2000	data reduction