3NFY | pdb_00003nfy

The Structure of Human Bisphosphoglycerate Mutase to 1.94A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T8P	1T8P.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	290	20% PEG 6K, 100mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.472	α = 90
b = 61.345	β = 95.87
c = 122.696	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 315r		2006-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.4	ESRF	ID14-4

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	1.94	122.169	95	0.062	0.062	15.4	3.6	40132	40132	0.047	0.047

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)
	1.94	2.04	84.9		0.281	0.281	2	3.4	5221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1T8P.pdb	1.94	54.81	42295	40076	2001	94.76	0.182	0.183	0.178	0.1803	0.277	0.2754	RANDOM	32.698

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]
-0.13		0.1	1.82		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.209
r_dihedral_angle_3_deg	18.184
r_dihedral_angle_4_deg	17.623
r_dihedral_angle_1_deg	6.554
r_scangle_it	4.583
r_scbond_it	3.085
r_mcangle_it	1.92
r_angle_refined_deg	1.882
r_mcbond_it	1.186
r_chiral_restr	0.151
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4074
Nucleic Acid Atoms
Solvent Atoms	1015
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection